Vegf-specific capture agents, compositions, and methods of using and making

ABSTRACT

The present application provides biligand and triligand protein-catalyzed capture (PCC) agents that specifically bind VEGF, as well as the use of these capture agents as detection, diagnosis, and treatment agents.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.13/601,023, filed Aug. 31, 2012, which claims priority to U.S.Provisional Patent Application No. 61/529,872, filed Aug. 31, 2011; U.S.Provisional Patent Application No. 61/556,713, filed Nov. 7, 2011; U.S.Provisional Patent Application No. 61/585,590, filed Jan. 11, 2012 andU.S. Provisional Patent Application No. 61/675,298, filed Jul. 24, 2012.The contents of the aforementioned applications are hereby incorporatedherein by reference in their entireties.

BACKGROUND

Detection of disease at the earliest stages requires multiplexmeasurements of key protein biomarkers in biological samples. Theavailability of high-affinity, highly selective compositions thatrecognize biomarkers from complex biological mixtures is a criticalcomponent for accurate detection of proteins that may indicate diseaseor changes in health.

Vascular endothelial growth factor A (VEGF) is a potent endothelialcell-specific mediator of angiogenesis and vasculogenesis. VEGF isinvolved pathologically in cancer, proliferative retinopathy, diseasepathology of wet form age-related macular degeneration (AMD), andrheumatoid arthritis, and as such represents an important diagnostic andtherapeutic target. VEGF signaling modulates angiogenesis, and VEGFlevels are elevated in a variety of tumor types. As such, VEGF presentsan attractive candidate for imaging, detection and treatment of cancer.

SUMMARY

Provided herein in certain embodiments are stable, synthetic VEGFcapture agents that specifically bind VEGF.

In certain embodiments, the VEGF capture agents provided herein comprisea designed anchor ligand and a designed secondary ligand, both of whichselectively bind VEGF. In certain embodiments, the capture agentsfurther comprise a designed tertiary ligand.

In certain embodiments, the VEGF capture agents provided herein arebiligands. In certain of these embodiments, the biligands comprise ananchor ligand comprising the amino acid sequence of SEQ ID NO:1 and asecondary ligand comprising the amino acid sequence of SEQ ID NOs:2, 3,or 4. In certain embodiments, the anchor ligand comprises an amino acidsequence, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98 or 100% identical to the amino acid sequence set forth inSEQ ID NO:1. In other embodiments, the anchor ligand comprises afragment of the amino acid sequence of SEQ ID NO:1. In certainembodiments, this fragment contains 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17 or 18 amino acids. In other embodiments, this fragmentcontains 5-18, 10-18, 5-15, 7-15, 9-15 or 3-16 amino acids. In certainembodiments, the secondary ligand comprises a formula of X2-X3-X4-X5-X6.In certain embodiments, X2 is selected from a positively charged D-aminoacid, an aromatic D-amino acid and a neutral D-amino acid. In otherembodiments, X2 is selected from D-arginine, D-tryptophan, D-leucine,D-valine, glycine, D-proline, D-isoleucine and D-alanine. In otherembodiments, X3 is selected from a neutral D-amino acid, an aromaticD-amino acid or a positively charged amino acid. In certain embodiments,X3 is selected from D-proline, D-phenylalanine, glycine, D-arginine,D-lysine, D-histidine, D-tryptophan and D-tyrosine. In otherembodiments, X4 is selected from a neutral D-amino acid, a positivelycharged D-amino acid, an aromatic D-amino acid and a polar D-amino acid.In certain embodiments, X4 is selected from D-isoleucine, D-leucine,D-proline, D-alanine, D-arginine, D-phenylalanine, D-threonine andD-histidine. In other embodiments, X5 is selected from a neutral D-aminoacid, a positively charged D-amino acid and a negatively charged D-aminoacid. In certain embodiments, X5 is selected from D-isoleucine, glycine,D-valine, D-leucine, D-alanine, D-proline, D-lysine, D-glutamate,D-histidine and D-arginine. In other embodiments, X6 is selected from apositively charged D-amino acid, an aromatic D-amino acid, a neutralD-amino acid and a polar D-amino acid. In certain embodiments, X6 isselected from D-arginine, D-lysine, D-tryptophan, D-tyrosine, D-proline,D-valine, glycine, D-isoleucine, D-alanine and D-glutamine.

In certain embodiments, X2 is selected from a positively charged D-aminoacid and an aromatic D-amino acid. In other embodiments, X2 is selectedfrom D-arginine and D-tryptophan. In other embodiments, X3 is selectedfrom a neutral D-amino acid and an aromatic D-amino acid. In certainembodiments, X3 is selected from D-proline, D-phenylalanine and glycine.In other embodiments, X4 is a neutral D-amino acid. In certainembodiments, X4 is selected from D-isoleucine, D-leucine, D-proline andD-alanine. In other embodiments, X5 is a neutral D-amino acid. Incertain embodiments, X5 is selected from D-isoleucine, glycine andD-valine. In other embodiments, X6 is a positively charged D-amino acid.In certain embodiments, X6 is selected from D-arginine and D-lysine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, D-valine, glycine andD-proline. In other embodiments, X3 is a positively charged amino acid.In certain embodiments, X3 is selected from D-arginine, D-lysine andD-histidine. In other embodiments, X4 is selected from a neutral D-aminoacid, a positively charged D-amino acid and an aromatic D-amino acid. Incertain embodiments, X4 is selected from D-proline, D-arginine andD-phenylalanine. In other embodiments, X5 is selected from a neutralD-amino acid and a positively charged D-amino acid. In certainembodiments, X5 is selected from D-leucine, D-isoleucine, D-alanine,D-proline and D-lysine. In other embodiments, X6 is selected from apositively charged D-amino acid, an aromatic D-amino acid and a neutralD-amino acid. In certain embodiments, X6 is selected from D-arginine,D-tryptophan, D-tyrosine, D-proline and D-valine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, glycine, D-proline,D-isoleucine and D-alanine. In other embodiments, X3 is an aromaticD-amino acid. In certain embodiments, X3 is selected from D-tryptophan,D-phenylalanine and D-tyrosine. In other embodiments, X4 is selectedfrom a positively charged D-amino acid, an aromatic D-amino acid and apolar D-amino acid. In certain embodiments, X4 is selected fromD-arginine, D-phenylalanine, D-threonine and D-histidine. In otherembodiments, X5 is selected from a neutral D-amino acid, a positivelycharged D-amino acid and a negatively charged D-amino acid. In certainembodiments, X5 is selected from glycine, D-alanine, D-proline,D-glutamate, D-histidine and D-arginine. In other embodiments, X6 isselected from a positively charged D-amino acid, an aromatic D-aminoacid, a neutral D-amino acid and a polar D-amino acid. In certainembodiments, X6 is selected from D-arginine, D-tryptophan, glycine,D-isoleucine, D-alanine and D-glutamine.

In other embodiments, the secondary ligand comprises an amino acidsequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20 and 21. In other embodiments, the secondary ligandcomprises an amino acid sequence, wherein one amino acid differs from anamino acid sequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20 and 21. In other embodiments, the secondaryligand comprises an amino acid sequence wherein the amino acid sequenceconsists of an amino acid sequence selected from SEQ ID NOs:2, 3, 4, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 and 21.

In certain embodiments, the anchor ligand and secondary ligand arelinked together via a 1,4-disubstituted-1,2,3-triazole (Tz4) linkage. Incertain embodiments, the biligands comprise a structure selected from:

In certain embodiments, the VEGF capture agents provided herein aretriligands. In certain of these embodiments, the triligands comprise ananchor ligand comprising the amino acid sequence of SEQ ID NO:1, asecondary ligand comprising the amino acid sequence of SEQ ID NO:3, anda tertiary ligand comprising the amino acid sequence of SEQ ID NOs:5, 6,7, or 8. In other embodiments, the anchor ligand comprises an amino acidsequence, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98 or 100% identical to the amino acid sequence set forth inSEQ ID NO:1. In other embodiments, the anchor ligand comprises afragment of the amino acid sequence of SEQ ID NO:1. In certainembodiments, this fragment contains 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17 or 18 amino acids. In other embodiments, this fragmentcontains 5-18, 10-18, 5-15, 7-15, 9-15 or 3-16 amino acids. In certainembodiments, the secondary ligand comprises a formula of X2-X3-X4-X5-X6.In certain embodiments, X2 is selected from a positively charged D-aminoacid, an aromatic D-amino acid and a neutral D-amino acid. In otherembodiments, X2 is selected from D-arginine, D-tryptophan, D-leucine,D-valine, glycine, D-proline, D-isoleucine and D-alanine. In otherembodiments, X3 is selected from a neutral D-amino acid, an aromaticD-amino acid or a positively charged amino acid. In certain embodiments,X3 is selected from D-proline, D-phenylalanine, glycine, D-arginine,D-lysine, D-histidine, D-tryptophan and D-tyrosine. In otherembodiments, X4 is selected from a neutral D-amino acid, a positivelycharged D-amino acid, an aromatic D-amino acid and a polar D-amino acid.In certain embodiments, X4 is selected from D-isoleucine, D-leucine,D-proline, D-alanine, D-arginine, D-phenylalanine, D-threonine andD-histidine. In other embodiments, X5 is selected from a neutral D-aminoacid, a positively charged D-amino acid and a negatively charged D-aminoacid. In certain embodiments, X5 is selected from D-isoleucine, glycine,D-valine, D-leucine, D-alanine, D-proline, D-lysine, D-glutamate,D-histidine and D-arginine. In other embodiments, X6 is selected from apositively charged D-amino acid, an aromatic D-amino acid, a neutralD-amino acid and a polar D-amino acid. In certain embodiments, X6 isselected from D-arginine, D-lysine, D-tryptophan, D-tyrosine, D-proline,D-valine, glycine, D-isoleucine, D-alanine and D-glutamine.

In certain embodiments, X2 is selected from a positively charged D-aminoacid and an aromatic D-amino acid. In other embodiments, X2 is selectedfrom D-arginine and D-tryptophan. In other embodiments, X3 is selectedfrom a neutral D-amino acid and an aromatic D-amino acid. In certainembodiments, X3 is selected from D-proline, D-phenylalanine and glycine.In other embodiments, X4 is a neutral D-amino acid. In certainembodiments, X4 is selected from D-isoleucine, D-leucine, D-proline andD-alanine. In other embodiments, X5 is a neutral D-amino acid. Incertain embodiments, X5 is selected from D-isoleucine, glycine andD-valine. In other embodiments, X6 is a positively charged D-amino acid.In certain embodiments, X6 is selected from D-arginine and D-lysine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, D-valine, glycine andD-proline. In other embodiments, X3 is a positively charged amino acid.In certain embodiments, X3 is selected from D-arginine, D-lysine andD-histidine. In other embodiments, X4 is selected from a neutral D-aminoacid, a positively charged D-amino acid and an aromatic D-amino acid. Incertain embodiments, X4 is selected from D-proline, D-arginine andD-phenylalanine. In other embodiments, X5 is selected from a neutralD-amino acid and a positively charged D-amino acid. In certainembodiments, X5 is selected from D-leucine, D-isoleucine, D-alanine,D-proline and D-lysine. In other embodiments, X6 is selected from apositively charged D-amino acid, an aromatic D-amino acid and a neutralD-amino acid. In certain embodiments, X6 is selected from D-arginine,D-tryptophan, D-tyrosine, D-proline and D-valine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, glycine, D-proline,D-isoleucine and D-alanine. In other embodiments, X3 is an aromaticD-amino acid. In certain embodiments, X3 is selected from D-tryptophan,D-phenylalanine and D-tyrosine. In other embodiments, X4 is selectedfrom a positively charged D-amino acid, an aromatic D-amino acid and apolar D-amino acid. In certain embodiments, X4 is selected fromD-arginine, D-phenylalanine, D-threonine and D-histidine. In otherembodiments, X5 is selected from a neutral D-amino acid, a positivelycharged D-amino acid and a negatively charged D-amino acid. In certainembodiments, X5 is selected from glycine, D-alanine, D-proline,D-glutamate, D-histidine and D-arginine. In other embodiments, X6 isselected from a positively charged D-amino acid, an aromatic D-aminoacid, a neutral D-amino acid and a polar D-amino acid. In certainembodiments, X6 is selected from D-arginine, D-tryptophan, glycine,D-isoleucine, D-alanine and D-glutamine.

In other embodiments, the secondary ligand comprises an amino acidsequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20 and 21. In other embodiments, the secondary ligandcomprises an amino acid sequence, wherein one amino acid differs from anamino acid sequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20 and 21. In other embodiments, the secondaryligand comprises an amino acid sequence wherein the amino acid sequenceconsists of an amino acid sequence selected from SEQ ID NOs:2, 3, 4, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 and 21.

In certain embodiments of the biligand and triligand capture agentsprovided herein, the tertiary ligand comprises a formula ofX2-X3-X4-X5-X6. In certain embodiments, X2 is a positively chargedD-amino acid. In other embodiments, X2 is selected from D-histidine,D-arginine and D-lysine. In other embodiments, X3 is selected from apolar D-amino acid, a neutral D-amino acid and a negatively chargedamino acid. In certain embodiments, X3 is selected from D-threonine,D-asparagine, D-leucine, D-proline, D-isoleucine, D-alanine, andD-glutamate. In other embodiments, X4 is selected from a positivelycharged D-amino acid, an aromatic D-amino acid and a neutral D-aminoacid. In certain embodiments, X4 is selected from D-histidine, D-lysine,D-arginine, D-tryptophan, D-phenylalanine, D-proline, D-leucine andD-tyrosine. In other embodiments, X5 is selected from a neutral D-aminoacid, a positively charged D-amino acid, an aromatic D-amino acid and apolar D-amino acid. In certain embodiments, X5 is selected fromD-valine, D-proline, D-histidine, D-phenylalanine, D-tryptophan,D-asparagine, D-glutamine, D-serine and D-tyrosine. In otherembodiments, X6 is selected from a positively charged D-amino acid, anaromatic D-amino acid, a polar D-amino acid and a neutral D-amino acid.In certain embodiments, X6 is selected from D-arginine, D-tyrosine,D-asparagine, D-glutamine, D-leucine, D-proline, D-lysine andD-histidine.

In certain embodiments, X2 is an aromatic D-amino acid. In otherembodiments, X2 is selected from D-tyrosine, D-phenylalanine andD-tryptophan. In other embodiments, X3 is selected from a neutralD-amino acid and a positively charged amino acid. In certainembodiments, X3 is selected from D-proline, D-alanine, glycine,D-leucine, D-lysine, D-arginine and D-histidine. In other embodiments,X4 is selected from a positively charged D-amino acid, an aromaticD-amino acid, a negatively charged D-amino acid, a neutral D-amino acidand a polar D-amino acid. In certain embodiments, X4 is selected fromD-arginine, D-histidine, D-tryptophan, D-phenylalanine, D-glutamate,D-proline, D-serine and D-threonine. In other embodiments, X5 isselected from a neutral D-amino acid, a negatively charged D-amino acid,a positively charged D-amino acid, an aromatic D-amino acid and a polarD-amino acid. In certain embodiments, X5 is selected from D-proline,D-aspartate, D-lysine, D-arginine, D-tyrosine, D-histidine, D-alanine,D-valine, D-leucine and D-asparagine. In other embodiments, X6 isselected from a positively charged D-amino acid, a polar D-amino acid, aneutral D-amino acid, a negatively charged D-amino acid and an aromaticD-amino acid. In certain embodiments, X6 is selected from D-histidine,D-lysine, D-asparagine, D-threonine, D-glutamine, D-leucine,D-aspartate, D-serine, D-tyrosine, D-arginine, D-tryptophan, D-glutamateand D-valine.

In certain embodiments, X2 is negatively charged D-amino acid. In otherembodiments, X2 is selected from D-glutamate and D-aspartate. In otherembodiments, X3 is selected from a negatively charged D-amino acid, anaromatic D-amino acid, a positively charged amino acid and a polarD-amino acid. In certain embodiments, X3 is selected from D-glutamate,D-phenylalanine, D-tryptophan, D-histidine, D-lysine, D-asparagine andD-serine. In other embodiments, X4 is selected from a neutral D-aminoacid, a positively charged D-amino acid, a polar D-amino acid, anegatively charged D-amino acid and an aromatic D-amino acid. In certainembodiments, X4 is selected from D-isoleucine, D-proline, D-alanine,D-arginine, D-serine, D-aspartate, D-asparagine, D-proline,D-phenylalanine, D-tyrosine and D-histidine. In other embodiments, X5 isselected from a positively charged D-amino acid, an aromatic D-aminoacid and a neutral D-amino acid. In certain embodiments, X5 is selectedfrom D-arginine, D-tyrosine, glycine, D-tryptophan, D-lysine,D-histidine, D-alanine, D-asparagine and D-leucine. In otherembodiments, X6 is selected from a negatively charged D-amino acid, aneutral D-amino acid, an aromatic D-amino acid and a polar D-amino acid.In certain embodiments, X6 is selected from D-aspartate, D-proline,D-tryptophan, D-tyrosine, D-leucine, D-asparagine, D-serine andD-threonine.

In other embodiments, the tertiary ligand comprises an amino acidsequence selected from SEQ ID NOs:5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64. In other embodiments, the secondary ligand comprises an aminoacid sequence, wherein one amino acid differs from an amino acidsequence selected from SEQ ID NOs:5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64. In other embodiments, the secondary ligand comprises an aminoacid sequence wherein the amino acid sequence consists of an amino acidsequence selected from SEQ ID NOs:5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64.

In certain embodiments, the anchor ligand and secondary ligand and/orthe secondary ligand and tertiary ligand are linked together via a Tz4linkage. In certain embodiments, the triligands comprise a structureselected from:

In certain embodiments, the VEGF capture agents provided herein arestable across a wide range of temperatures, pH's, storage times, storageconditions, and reaction conditions, and in certain embodiments thecapture agents are more stable than a biologic. In certain embodiments,the capture agents are stable in storage as a lyophilized powder. Incertain embodiment, the capture agents are stable in storage at atemperature of about −80° C. to about 40° C. In certain embodiments, thecapture agents are stable in storage at room temperature. In certainembodiments, the capture agents are stable in human serum for at least24 hours. In certain embodiments, the capture agents are stable at a pHin the range of about 3 to about 8.

In certain embodiments, the VEGF capture agents provided herein compriseone or more detectable labels. In certain of these embodiments, thelabel is copper-DOTA. In other embodiments, the label is a fluorescentlabel. In other embodiments, the detectable label is ⁶⁴Cu DOTA, ⁶⁸GaDOTA, ¹⁸F, ⁶⁴Cu, ⁶⁸Ga, ⁸⁹Zr, ¹²⁴I, ⁸⁶Y, ^(94m)Tc, ^(110m)In, ¹¹C or⁷⁶Br.

In certain embodiments, kits are provided that comprise one or more ofthe VEGF capture agents provided herein. In certain of theseembodiments, the kits include instructions for use.

In certain embodiments, methods are provided for identifying, detecting,quantifying, or separating VEGF in a biological sample using the captureagents provided herein. In certain embodiments, these methods areimmunoassays where the VEGF capture agent is used as a replacement foran antibody or its equivalent. In certain embodiments, the immunoassayis a Western blot, pull-down assay, dot blot, or ELISA.

In certain embodiments, methods are provided for diagnosing orclassifying a condition associated with increased VEGF expression and/oractivity in a subject in need thereof using the capture agents providedherein. In certain of these embodiments, the condition is cancer, andthe methods are used to diagnose and/or stage the cancer. In certainembodiments, this condition is selected from cancer, proliferativeretinopathy, disease pathology of wet form age-related maculardegeneration (AMD), or rheumatoid arthritis.

In certain embodiments, methods are provided for treating a conditionassociated with increased VEGF expression and/or activity in a subjectin need thereof. In certain embodiments, these methods compriseadministering to a subject a therapeutically effective amount of a VEGFcapture agent as provided herein. In certain embodiments, the conditionbeing treated is cancer, proliferative retinopathy, disease pathology ofwet-form AMD, or rheumatoid arthritis. In certain embodiments, the VEGFcapture agents provided herein function as immunotherapeutics.

In certain embodiments, methods are provided for inhibiting VEGFactivity in vivo or in vitro using a VEGF capture agent as providedherein.

In certain embodiments, methods are provided for inhibiting binding ofVEGF to VEGF receptor (VEGFR) using a VEGF capture agent as providedherein.

In certain embodiments, methods are provided for inhibiting VEGFRsignaling using a VEGF capture agent as provided herein.

In certain embodiments, the use of one or more VEGF capture agents isprovided for use in preparing a medicament for treating a conditionassociated with increased VEGF expression and/or activity in a subjectin need thereof.

In certain embodiments, methods are provided for synthesizing the VEGFcapture agents disclosed herein.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1: In situ click chemistry protocol.

FIG. 2: In situ click chemistry protocol.

FIG. 3: Structure of anchor ligand comprising the amino acid sequence ofSEQ ID NO:1 (VEPNCDIHVMWEWECFERL). The underline represents disulfiderestrained residues.

FIG. 4: Structure of the anchor ligand construct Biotin-PEG-anchorligand-Az4.

FIG. 5: Informatic clustering guides candidate selection for secondaryand tertiary ligands. Different regions of the protein epitope aresuggested to be sampled by different clusters. Dark blue=5-mer secondaryligand hits from biligand screen.

FIG. 6: Structure of the biligand constructBiotin-PEG-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Az4.

FIG. 7: Informatic clustering guides candidate selection for secondaryand tertiary ligands. Different regions of the protein epitope aresuggested to be sampled by different clusters. Dark blue=5-mer tertiaryligand hits from triligand screen.

FIG. 8: Structure of Biligand 1, which comprises the anchor ligand ofSEQ ID NO:1 and the secondary ligand of SEQ ID NO:2 (rplir).

FIG. 9: Structure of Biligand 2, which comprises the anchor ligand ofSEQ ID NO:1 and the secondary ligand of SEQ ID NO:3 (lfrew).

FIG. 10: Structure of Biligand 3, which comprises the anchor ligand ofSEQ ID NO:1 and the secondary ligand of SEQ ID NO:4 (fsrkte).

FIG. 11: Structure of Triligand 1, which comprises the anchor ligand ofSEQ ID NO:1, the secondary ligand of SEQ ID NO:3, and the tertiaryligand of SEQ ID NO:5 (frsvn).

FIG. 12: Structure of Triligand 2, which comprises the anchor ligand ofSEQ ID NO:1, the secondary ligand of SEQ ID NO:3, and the tertiaryligand of SEQ ID NO:6 (eeird).

FIG. 13: Structure of Triligand 3, which comprises the anchor ligand ofSEQ ID NO:1, the secondary ligand of SEQ ID NO:3, and the tertiaryligand of SEQ ID NO:7 (hthwl).

FIG. 14: Structure of Triligand 4, which comprises the anchor ligand ofSEQ ID NO:1, the secondary ligand of SEQ ID NO:3, and the tertiaryligand of SEQ ID NO:8 (ewsrw).

FIG. 15: Binding of Triligand 2 (“Trilig2-lfrew-eeird”), Triligand 3(“Trilig3-hthwl-hthwl”), Biligand 2 (“Bilig2-lfrew”), the anchor ligand(“Anchor”) component of the bi- and triligands, Avastin®, and Avastin®Fab to VEGF165 as measured by ELISA.

FIG. 16: Binding of Triligand 1 (“Trilig1-lfrew-frsvn”), Triligand 2(“Trilig2-lfrew-eeird”), Triligand 3 (“Trilig3-lfrew-hthwl”), Triligand4 (“Trilig4-lfrew-ewsrw”), Biligand 2 (“Bilig2-lfrew”), the anchorligand (“Anchor”) component of the bi- and triligands, and Avastin® toVEGF165 as measured by capture agent immunoprecipitation fromVEGF165-spiked buffer (“B”) and VEGF165-spiked human serum (“S”).Results were analyzed by silver stain (top panel) and Western blot(bottom panel).

FIG. 17: HPLC analysis of in vitro stability for anti-VEGF PCC triligandat 37° C. (A) In 25% (v/v) human AB male serum. (B) In TBS pH 7.25. ThePCC (200 μg) was incubated at 37° C. in the presence or absence of 25%(v/v) human AB male serum (HS-20, Omega Scientific, Tarzana, Calif.) inTBS. Aliquots were taken at various time points. The PCC was separatedfrom plasma proteins on a Microcon centrifugal filter device (MicroconYM-10, MWCO=10 kDa, Millipore, Bedford, Mass.) by centrifugation at12,000 rpm. The filtrates were examined by analytical HPLC on a C₁₈column.

FIG. 18: Inhibition of HUVEC proliferation by Biligand 1(“Bilig1(rplir)”), Biligand 2 (“Bilig2 (lfrew)”), Biligand 3 (“Bilig3-fsrkte”),the anchor ligand (“Anchor”) of the biligands, and Avastin®.

FIG. 19: A. Concentration-time profile after IV administration (1 mg/kg)of Biligand 1 to mice. Calculated T_(1/2)=7.2613 minutes (3 points,uniform weighting). B. Concentration-time profile after IPadministration (5 mg/kg) of Biligand 1 to mice. CalculatedT_(1/2)=154.3283 minutes (2 points, uniform weighting).

FIG. 20: Inhibition of VEGF165 binding to VEGFR2 by Triligand 2(“Trilig2-lfrew-eeird”), Triligand 3 (“Trilig3-lfrew-hthwl”), Biligand 2(“Bilig2-lfrew”), the anchor ligand (“Anchor”) of the bi- andtriligands, and Avastin® Fab as measured by competitive ELISA.

FIG. 21: Inhibition of VEGF165 binding to Avastin® Fab by Triligand 1(“Trilig1-lfrew-frsvn”), Triligand 2 (“Trilig2-lfrew-eeird”), Triligand3 (“Trilig3-lfrew-hthwl”), and Biligand 2 (“Bilig2-lfrew”) as measuredby competitive ELISA.

FIG. 22: Plasma protein binding by Biligand 2 (“Bilig2-lfrew”), Biligand3 (“Bilig3-fsrkte”), the anchor ligand (“Anchor”) of the biligands andthe reference compounds octreotide and warfarin.

FIG. 23: Stability of Biligand 1 (“Bilig1-rplir”), Biligand 2(“Bilig2-lfrew”), Biligand 3 (“Bilig3-fsrkte”), the anchor ligand(“Anchor”) of the biligands, and the reference compounds octreotide,propantheline, and propanolol in human plasma and mouse liver microsomesas measured by HPLC and MS/MS.

FIG. 24: Method for preparing tetrameric form of Triligand 2.

FIG. 25: Method for preparing DOTA-labeled tetrameric form of Triligand2 by assembling bifunctional (DOTA- and biotin-conjugated) Triligand 2on streptavidin scaffold.

FIG. 26: Structure of bifunctional (DOTA- and biotin-conjugated)Triligand 2.

FIG. 27: Method for preparing DOTA-labeled tetrameric form of Triligand2 by assembling using chemical modification of an engineeredstreptavidin scaffold.

FIG. 28: Structure of biotin-conjugated Triligand 2.

FIG. 29: Method for preparing multimeric capture agent via amide bondformation.

FIG. 30: Structure of Triligand 2 homodimer prepared by amide bondformation.

FIG. 31: Method for preparing multimeric capture agent via CuAAC.

FIG. 32: Structure of Triligand 2 homodimer prepared by CuAAC.

FIG. 33: Structure of Triligand 2/Triligand 3 heterodimer joined viaCuAAC.

FIG. 34: Structure of X-Triligand 2, where X is Ac, biotin-PEG,DOTA-PEG, etc.

FIG. 35: Synthesis of PEGylated Triligand 2.

FIG. 36: Synthesis of PEGylated Triligand 2.

FIG. 37: Synthesis of multimeric Triligand 2.

FIG. 38: Synthesis of multimeric Triligand 2 (homotetramer).

FIG. 39: Inhibition of VEGF165 binding to VEGFR2 by modified C-terminusTriligand 2 as measured by competitive ELISA.

FIG. 40: Inhibition of VEGF165 binding to VEGFR2 by multimeric Triligand2 as measured by competitive ELISA.

FIG. 41: Binding affinity of multimeric Triligand 2.

FIG. 42: Comparison of triligand modifications by VEGF pull-down assay.L: MW ladder; 1 B/S: Triligand 2-NH₂; 2B/S: Triligand 2-OH; 3B/S:Triligand 2-PEG40 KD; 4B/S: Triligand 2-branched PEG40 KD; C: VEGFcontrol (50 ng).

FIG. 43: Comparison of triligand modifications by VEGF pull-down assay.L: MW ladder; 1 B/S: Triligand 2-NH₂; 2B/S: PEG2arm-Triligand 2 (dimer);3B/S: PEG4arm-Triligand 2 (tetramer); C: VEGF control (50 ng).

FIG. 44: Biodistribution study results for mouse 1009. A. Maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, scaled to fixed percentile of image. B. Cropped MIPs.Gaussian filter (0.100 mm FWHM) applied to the images, scaled to fixedpercentile of image. C. Cropped coronal slices. Gaussian filter (0.100mm FWHM) applied to the images. D. Tumors extracted using 3D ROI Tool invivoQuant™. Left tumor is in red, right tumor is in green. E. MIP ofextracted tumors. At 240 minutes, the color scale min (black) was 0 andthe color scale max (white) was 3.9×10-5 μCi. At 1200 minutes, the colorscale min (black) was 0 and the color scale max (white) was 1.63×10-5μCi (corrected for isotope decay).

FIG. 45: Biodistribution study results for mouse 1010. A. Maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, scaled to fixed percentile of image. B. Cropped MIPs.Gaussian filter (0.100 mm FWHM) applied to the images, scaled to fixedpercentile of image. C. Cropped coronal slices. Gaussian filter (0.100mm FWHM) applied to the images. D. Tumors extracted using 3D ROI Tool invivoQuant™. Left tumor is in red, right tumor is in green. E. MIP ofextracted tumors. At 240 minutes, the color scale min (black) was 0 andthe color scale max (white) was 3.9×10-5 μCi. At 1200 minutes, the colorscale min (black) was 0 and the color scale max (white) was 1.63×10-5μCi (corrected for isotope decay).

FIG. 46: Biodistribution study results for mouse 1011. A. Maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, scaled to fixed percentile of image. B. Cropped MIPs.Gaussian filter (0.100 mm FWHM) applied to the images, scaled to fixedpercentile of image. C. Cropped coronal slices. Gaussian filter (0.100mm FWHM) applied to the images. D. Tumors extracted using 3D ROI Tool invivoQuant™. Left tumor is in red, right tumor is in green. E. MIP ofextracted tumors. At 240 minutes, the color scale min (black) was 0 andthe color scale max (white) was 3.9×10-5 μCi. At 1200 minutes, the colorscale min (black) was 0 and the color scale max (white) was 1.63×10-5μCi (corrected for isotope decay).

FIG. 47: Biodistribution study results for mouse 1012. A. Maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, scaled to fixed percentile of image. B. Cropped MIPs.Gaussian filter (0.100 mm FWHM) applied to the images, scaled to fixedpercentile of image. C. Cropped coronal slices. Gaussian filter (0.100mm FWHM) applied to the images. D. Tumors extracted using 3D ROI Tool invivoQuant™. Left tumor is in red, right tumor is in green. E. MIP ofextracted tumors. At 240 minutes, the color scale min (black) was 0 andthe color scale max (white) was 3.9×10-5 μCi. At 1200 minutes, the colorscale min (black) was 0 and the color scale max (white) was 1.63×10-5μCi (corrected for isotope decay).

FIG. 48: Biodistribution results for mouse 1102. A. Cropped coronalslices. Left=HT29, right MSTO-211 H. Gaussian filter (0.100 mm FWHM)applied to the images, scaled to fixed max. B. Cropped coronal slices.Left=HT29, right MSTO-211 H. Gaussian filter (0.100 mm FWHM) applied tothe images, scaled to decay-corrected fixed max.

FIG. 49: Biodistribution results for mouse 1004. A. Cropped coronalslices. Left=HT29, right MSTO-211 H. Gaussian filter (0.100 mm FWHM)applied to the images, scaled to fixed max. B. Cropped coronal slices.Left=HT29, right MSTO-211 H. Gaussian filter (0.100 mm FWHM) applied tothe images, scaled to decay-corrected fixed max.

FIG. 50: Method for preparing horseradish peroxidase (HRP)-labeledtetrameric form of Triligand 2 by assembling biotinylated Triligand 2 onHRP-conjugated streptavidin scaffold.

FIG. 51: Biodistribution results for mouse 1114R. Left=HT29. Resultswere corrected for isotope decay.

FIG. 52: Biodistribution results for mouse 1017. Left=HT29. Results werecorrected for isotope decay.

FIG. 53: Biodistribution results for mouse 1022. Left=HT29. Results werecorrected for isotope decay.

FIG. 54: Biodistribution results for mice 1013, 1015, 1016, and 1114R(control) and 1021-1024 (48 hour Avastin® blockade) at 20 hourspost-VEGF triligand administration. Left=HT29.

FIG. 55: Tumor versus heart tissue distribution of Example 17.

FIG. 56: Tumor versus other tissue distribution of Example 17.

FIG. 57: Biodistribution results for mice 1009 and 1011 (control) and1010 and 1012 (24 hour Avastin® blockade) at 20 hours post-VEGFtriligand administration. Left=HT29, right=MSTO-211 H.

FIG. 58: Biodistribution study results for mouse 1013. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI Tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 59: Biodistribution study results for mouse 1014. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI Tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 60: Biodistribution study results for mouse 1017. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI Tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 61: Biodistribution study results for mouse 1018. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI Tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 62: Biodistribution study results for mouse 1021. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 63: Biodistribution study results for mouse 1022. A. Kidney maximumintensity projections (MIPs). Gaussian filter (0.200 mm FWHM) applied tothe images, color scale max corrected for isotope decay. B. Tumorcropped MIPs. Gaussian filter (0.200 mm FWHM) applied to the images,color scale max corrected for isotope decay. C. Tumor cropped coronalslices. Gaussian filter (0.200 mm FWHM) applied to the images, colorscale max corrected for isotope decay. D. Tumors extracted using 3D ROITool in vivoQuant™. Gaussian filter (0.200 mm FWHM) applied to theimages, color scale max corrected for isotope decay. E. MIP of extractedtumors using 3D ROI Tool in vivoQuant™. Gaussian filter (0.200 mm FWHM)applied to the images, color scale max corrected for isotope decay.

FIG. 64: Mean (±SD) plasma concentrations (ng/mL) of VEGF-PCC followinga single intravenous (IV) or intraperitoneal (IP) dose in mouse.

FIG. 65: Copper catalyzed azide/alkyne cycloaddition (CuAAC) between afully protected alkyne containing amino acid and a fully protected azidecontaining amino acid to provide a protected 1,4-triazole linkeddipeptide.

FIG. 66: (A) Hit sequences obtained from the biligand screen with acomprehensive library. (B) Biligand structure illustrating the anchor(red) and selected secondary ligands (blue). These sequences are SEQ IDNOs:9, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 3, 20 and 21 readingfrom top to bottom.

FIG. 67: Affinities of anti-VEGF PCC biligand candidates versus anchor.VEGF165A was immobilized on NUNC MaxiSorp plates and incubated withvarying concentrations of biotinylated peptide. All values werenormalized to the binding observed at saturation.

FIG. 68: Immunoprecipitation by anti-VEGF PCC biligand candidates vs.anchor from buffer and human serum. Biotinylated ligands were incubatedwith 0.5 μg/mL VEGF165A in PBS pH 7.4 (P) or 25% (v/v) human serum (S)for 16 h at 4° C., after which DynaBeads® M-280 Streptavidin were addedfor 3 h at 4° C. Beads were washed exhaustively, eluted with SDS-PAGELaemmli sample buffer, and analyzed for VEGF165A by Western blottingcompared to control (50 ng VEGF).

FIG. 69: (A) Hit sequences obtained from the triligand screen with acomprehensive library. These sequences are SEQ ID NOs:22, 23, 24, 25, 7,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 5, 48, 49, 50, 6, 51, 52, 53, 8, 54, 55, 56, 57, 58, 59,60, 61, 62, 63 and 64 reading from top to bottom and left to rightacross the three columns. (B) Triligand structure illustrating theanchor (red), secondary ligand (blue), and selected tertiary ligands(green).

FIG. 70: Affinities of anti-VEGF PCC triligand candidates. VEGF165A wasimmobilized on NUNC MaxiSorp plates and incubated with varyingconcentrations of biotinylated PCC or bevacizumab (mAb or Fab). Allvalues were normalized to the binding observed at saturation.

FIG. 71: Immunoprecipitation by anti-VEGF PCC triligand candidates frombuffer and human serum. Biotinylated ligands were incubated with 0.5μg/mL VEGF165A in PBS pH 7.4 (P) or 25% (v/v) human serum (S) for 16 hat 4° C., after which DynaBeads® M-280 Streptavidin were added for 3 hat 4° C. Beads were washed exhaustively, eluted with SDS-PAGE Laemmlisample buffer, and analyzed for VEGF165A by Western blotting compared tocontrol (50 ng VEGF).

FIG. 72: Inhibition of VEGF binding to VEGFR2 by anti-VEGF PCC triligandcandidates. Receptor blocking activities were screened by measuringbiotinylated VEGF165A binding to VEGFR2-coated wells in the presence ofserial dilutions of PCC or bevacizumab Fab. All values were normalizedto the binding observed at saturation.

FIG. 73: Silver-stained gel visualizing total immunoprecipitatedprotein. Biotinylated ligands were incubated with 0.5 μg/mL VEGF165A inPBS pH 7.4 (P) or 25% (v/v) human serum (S) for 16 h at 4° C., afterwhich DynaBeads® M-280 Streptavidin were added for 3 h at 4° C. Beadswere washed exhaustively, eluted with SDS-PAGE Laemmli sample buffer,and analyzed by SDS-PAGE (12% gel) with silver staining.

FIG. 74: Tissue distribution of ⁶⁴Cu-DOTA-triligand in HT-29xenograft-bearing nude mice after intraperitoneal injection. PercentID/g was calculated from microPET images acquired at 4 and 20 h postinjection. For blocking human VEGF-A, unlabeled bevacizumab (1 mg) wasadministered i.v. 48 h prior to ⁶⁴Cu-DOTA-triligand. The data representsthe average levels±SD from 4 mice per time point.

FIG. 75: Representative chromatogram of IN-VT-1001 in mouse plasmaAnimal Number 27 (IP), 120 minutes.

FIG. 76: Schematic of the reaction of the C-terminus of the triligandwith a 4-arm PEG derivative (MW 40,000; Jenkem #4ARM-NH2-40K) resultingin the formation of a homotetramer.

DETAILED DESCRIPTION OF THE INVENTION

The following description of the invention is merely intended toillustrate various embodiments of the invention. As such, the specificmodifications discussed are not to be construed as limitations on thescope of the invention. It will be apparent to one skilled in the artthat various equivalents, changes, and modifications may be made withoutdeparting from the scope of the invention, and it is understood thatsuch equivalent embodiments are to be included herein.

ABBREVIATIONS

AMD, age-related macular degeneration; Az4,6-azido-L-norleucine; CuAAC,copper catalyzed azide/alkyne cycloaddition; DIEA,N-hydroxy-7-aza-benzotriazole (HOAt), or diisopropylethylamine; HATU,O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluroniumhexafluorophosphate; HBTU,O-Benzotriazole-N,N,N′,N′-tetramethyl-uronium-hexafluoro-phosphate; NMP,1-methyl-2-pyrrolidinone; OBOC, one-bead-one-compound; TIS,triisopropylsilane; TFA, trifluoroacetic acid; Tz4,1,4-disubstituted1,2,3-triazole; VEGF, vascular endothelial growth factor; VEGFR,vascular endothelial growth factor receptor.

DEFINITIONS

The term “capture agent” as used herein refers to a protein-catalyzedcapture (PCC) agent that comprises one or more target-binding moietiesand which specifically binds to a target protein via thosetarget-binding moieties. Each target-binding moiety exhibits bindingaffinity for the target protein, either individually or in combinationwith other target-binding moieties. In certain embodiments, eachtarget-binding moiety binds to the target protein via one or morenon-covalent interactions, including for example hydrogen bonds,hydrophobic interactions, and van der Waals interactions. A captureagent may comprise one or more organic molecules, including for examplepolypeptides, peptides, polynucleotides, and other non-polymericmolecules.

The terms “polypeptide,” “peptide,” and “protein” are usedinterchangeably herein to refer to an amino acid sequence comprising apolymer of amino acid residues. The terms apply to amino acid polymersin which one or more amino acid residues is an artificial chemicalmimetic of a corresponding naturally occurring amino acid, as well as tonaturally occurring amino acid polymers and non-naturally occurringamino acid polymers.

The term “amino acid” refers to naturally occurring and synthetic aminoacids, as well as amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids, andisomers thereof. Naturally occurring amino acids are those encoded bythe genetic code, as well as those amino acids that are later modified,e.g., hydroxyproline, carboxyglutamate, O-phosphoserine, and isomersthereof. The term “amino acid analogs” refers to compounds that have thesame basic chemical structure as a naturally occurring amino acid, i.e.,a carbon that is bound to a hydrogen, a carboxyl group, an amino group,and an R group, e.g., homoserine, norleucine, methionine sulfoxide,methionine methyl sulfonium. Such analogs have modified R groups (e.g.,norleucine) or modified peptide backbones, but retain the same basicchemical structure as a naturally occurring amino acid. The term “aminoacid mimetics” refers to chemical compounds that have a structure thatis different from the general chemical structure of an amino acid, butthat functions in a manner similar to a naturally occurring amino acid.Amino acids may be referred to herein by either their commonly knownthree letter symbols or by the one-letter symbols recommended by theIUPAC-IUB Biochemical Nomenclature Commission.

The term “non-natural amino acid” as used herein refers to an amino acidthat is different from the twenty naturally occurring amino acids(alanine, arginine, glycine, asparagine, aspartic acid, cysteine,glutamine, glutamic acid, serine, threonine, histidine, lysine,methionine, proline, valine, isoleucine, leucine, tyrosine, tryptophan,phenylalanine) in its side chain functionality. The non-natural aminoacid can be a close analog of one of the twenty natural amino acids, orit can introduce a completely new functionality and chemistry, as longas the hydrophobicity of the non-natural amino acid is either equivalentto or greater than that of the natural amino acid. The non-natural aminoacid can either replace an existing amino acid in a protein(substitution), or be an addition to the wild type sequence (insertion).The incorporation of non-natural amino acids can be accomplished byknown chemical methods including solid-phase peptide synthesis or nativechemical ligation, or by biological methods.

The terms “specific binding,” “selective binding,” “selectively binds,”or “specifically binds” as used herein refer to non-random binding of abinding agent such as a capture agent to an epitope on a predeterminedantigen. Typically, the binding agent binds with an affinity (KD) ofapproximately less than 10-′ M, such as approximately less than 10⁻⁸ M,10⁻⁹ M or 10⁻¹⁰ M or even lower.

The term “KD” as used herein refers to the dissociation equilibriumconstant of a particular interaction between a binding agent such as acapture agent and its antigen. Typically, the capture agents of theinvention bind to VEGF with a dissociation equilibrium constant (KD) ofless than approximately 10-′ M, such as less than approximately 10⁻⁸ M,10⁻⁹ M or 10⁻¹⁰ M or even lower, for example, as determined usingsurface plasmon resonance (SPR) technology in a Biacore instrument usingthe antigen as the ligand and the capture agent as the analyte, andbinds to the predetermined antigen with an affinity corresponding to aKD that is at least ten-fold lower, such as at least 100 fold lower, forinstance at least 1,000 fold lower, such as at least 10,000 fold lower,for instance at least 100,000 fold lower than its affinity for bindingto a non-specific antigen (e.g., BSA, casein) other than thepredetermined antigen or a closely-related antigen. The amount withwhich the affinity is lower is dependent on the KD of the capture agent,so that when the KD of the capture agent very low (that is, the captureagent is highly specific), then the amount with which the affinity forthe antigen is lower than the affinity for a non-specific antigen may beat least 10,000 fold.

The term “kd” (sec’) as used herein refers to the dissociation rateconstant of a particular binding agent-antigen interaction. Said valueis also referred to as the koff value.

The term “ka” (M-‘xsec’) as used herein refers to the association rateconstant of a particular binding agent-antigen interaction.

The term “KD” (M) as used herein refers to the dissociation equilibriumconstant of a particular binding agent-antigen interaction.

The term “KA” (M-′) as used herein refers to the association equilibriumconstant of a particular binding agent-antigen interaction and isobtained by dividing the ka by the kd.

The term “condition” as used herein refers generally to a disease,event, or a change in health status. A change in health status may beassociated with a particular disease or event, in which case the changemay occur simultaneously with or in advance of the disease or event. Inthose cases where the change in health status occurs in advance of adisease or event, the change in health status may serve as a predictorof the disease or event. For example, a change in health status may bean alteration in the expression level of a particular gene associatedwith a disease or event. Alternatively, a change in health status maynot be associated with a particular disease or event.

The terms “treat,” “treating,” or “treatment” as used herein with regardto a condition refer to preventing the condition; slowing the onset,occurrence, or rate of development of the condition; reducing the riskof developing or experiencing the condition; preventing or delaying thedevelopment of symptoms associated with the condition; permanently ortemporarily reducing or ending symptoms associated with the condition;lessening the severity of the condition; or some combination thereof.

A “therapeutically effective amount” as used herein refers to an amounteffective, at dosages and for periods of time necessary, to achieve adesired therapeutic result. A therapeutically effective amount may varyaccording to factors such as disease state, age, sex, and weight of theindividual, and the ability of the capture agent to elicit a desiredresponse in the individual.

The term “vascular endothelial growth factor” or “VEGF” as used hereinrefers to any splicing isoform of VEGF-A, including VEGF121, VEGF165,VEGF189, and VEGF206, or a portion thereof such as an epitope.

The term “antibody” as used herein refers to a protein of the kind thatis produced by activated B cells after stimulation by an antigen and canbind specifically to the antigen promoting an immune response inbiological systems. Full antibodies typically consist of four subunitsincluding two heavy chains and two light chains. The term antibodyincludes natural and synthetic antibodies, including but not limited tomonoclonal antibodies, polyclonal antibodies or fragments thereof.Exemplary antibodies include IgA, IgD, IgG1, IgG2, IgG3, IgM and thelike. Exemplary fragments include Fab, Fv, Fab′, F(ab′)2 and the like. Amonoclonal antibody is an antibody that specifically binds to and isthereby defined as complementary to a single particular spatial andpolar organization of another biomolecule which is termed an “epitope.”In some forms, monoclonal antibodies can also have the same structure. Apolyclonal antibody refers to a mixture of different monoclonalantibodies. In some forms, polyclonal antibodies can be a mixture ofmonoclonal antibodies where at least two of the monoclonal antibodiesbinding to a different antigenic epitope. The different antigenicepitopes can be on the same target, different targets, or a combination.Antibodies can be prepared by techniques that are well known in the art,such as immunization of a host and collection of sera (polyclonal) or bypreparing continuous hybridoma cell lines and collecting the secretedprotein (monoclonal).

The term “stable” as used herein with regard to a capture agent orpharmaceutical formulation thereof means that the agent or formulationmaintains structural and functional integrity for a sufficient period oftime to be useful in the methods described herein.

The term “synthetic” as used herein with regard to a capture agent meansthat the capture agent has been generated by chemical rather thanbiological means. Synthetic capture agents are specifically designedusing bioinformatic analytical tools to define aspects of the structure.The anchor ligands are selected from a pool of potential anchor ligandsbased on inherent properties.

Unless otherwise stated, sequence identity/similarity values providedherein refer to the value obtained using the BLAST 2.0 suite of programsusing default parameters (Altschul, et al., (1997) Nucleic Acids Res.25:3389-402).

As those of ordinary skill in the art will understand, BLAST searchesassume that proteins can be modeled as random sequences. However, manyreal proteins comprise regions of nonrandom sequences, which may behomopolymeric tracts, short-period repeats, or regions enriched in oneor more amino acids. Such low-complexity regions may be aligned betweenunrelated proteins even though other regions of the protein are entirelydissimilar. A number of low-complexity filter programs can be employedto reduce such low-complexity alignments. For example, the SEG (Wootenand Federhen, (1993) Comput. Chem. 17:149-63) and XNU (Claverie andStates, (1993) Comput. Chem. 17:191-201) low-complexity filters can beemployed alone or in combination.

As used herein, “sequence identity” or “identity” in the context of twonucleic acid or polypeptide sequences includes reference to the residuesin the two sequences, which are the same when aligned for maximumcorrespondence over a specified comparison window. When percentage ofsequence identity is used in reference to proteins it is recognized thatresidue positions which are not identical often differ by conservativeamino acid substitutions, where amino acid residues are substituted forother amino acid residues with similar chemical properties (e.g., chargeor hydrophobicity) and therefore do not change the functional propertiesof the molecule. Where sequences differ in conservative substitutions,the percent sequence identity may be adjusted upwards to correct for theconservative nature of the substitution. Sequences, which differ by suchconservative substitutions, are said to have “sequence similarity” or“similarity.” Means for making this adjustment are well known to thoseof skill in the art. Typically this involves scoring a conservativesubstitution as a partial rather than a full mismatch, therebyincreasing the percentage sequence identity. Thus, for example, where anidentical amino acid is given a score of 1 and a non-conservativesubstitution is given a score of zero, a conservative substitution isgiven a score between zero and 1. The scoring of conservativesubstitutions is calculated, e.g., according to the algorithm of Meyersand Miller, (1988) Computer Applic. Biol. Sci. 4:11-17, e.g., asimplemented in the program PC/GENE (Intelligenetics, Mountain View,Calif., USA).

As used herein, “percentage of sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison and multiplying the result by 100 to yield the percentage ofsequence identity.

The term “substantial identity” of polynucleotide sequences means that apolynucleotide comprises a sequence that has between 50-100% sequenceidentity, preferably at least 50% sequence identity, preferably at least60% sequence identity, preferably at least 70%, more preferably at least80%, more preferably at least 90% and most preferably at least 95%,compared to a reference sequence using one of the alignment programsdescribed using standard parameters. One of skill will recognize thatthese values can be appropriately adjusted to determine correspondingidentity of proteins encoded by two nucleotide sequences by taking intoaccount codon degeneracy, amino acid similarity, reading framepositioning and the like. Substantial identity of amino acid sequencesfor these purposes normally means sequence identity of between 55-100%,preferably at least 55%, preferably at least 60%, more preferably atleast 70%, 80%, 90% and most preferably at least 95%.

Development of VEGF Capture Agents:

In situ click chemistry (Manetsch 2004; Mocharla 2004; Whiting 2006) isa technique in which a small molecule enzymatic inhibitor is separatedinto two moieties, each of which is then expanded into a smalllibrary—one containing acetylene functionalities, and the othercontaining azide groups. The enzyme itself then assembles the ‘best fit’inhibitor from these library components by selectively promoting1,3-dipolar cycloaddition between the acetylene and azide groups to forma triazole linkage (the ‘click’ reaction). The enzyme promotes the clickreaction only between those library components that bind to the proteinin the right orientation. The resultant inhibitor can exhibit farsuperior affinity characteristics relative to the initial inhibitor thatformed the basis of the two libraries (Jencks 1981; Murray 2002).

Sequential in situ click chemistry extends the in situ click chemistryconcept to enable the discovery of multiligand capture agents. Thisprocess was used previously to produce a triligand capture agent againstthe model protein carbonic anhydrase II (CAII) (Agnew 2009). Sequentialin situ click chemistry has several advantages. First, structuralinformation about the protein target is replaced by the ability tosample a very large chemical space to identify the ligand components ofthe capture agent. For example, an initial ligand may be identified byscreening the protein against a large (>10⁶ element)one-bead-one-compound (OBOC) (Lam 1991) peptide library, where thepeptides themselves may be comprised of natural, non-natural, and/orartificial amino acids. The resultant anchor ligand is then utilized inan in situ click screen, again using a large OBOC library, to identify abiligand binder. A second advantage is that the process can be repeated,so that the biligand is used as an anchor to identify a triligand, andso forth. The final capture agent can then be scaled up using relativelysimple and largely automated chemistries, and it can be developed with alabel, such as a biotin group, as an intrinsic part of its structure.This approach permits the exploration of branched, cyclic, and linearcapture agent architectures. While many strategies for protein-directedmultiligand assembly have been described (Shuker 1996; Erlanson 2000),most require detailed structural information on the target to guide thescreening strategy, and most (such as the original in situ clickapproach), are optimized for low-diversity small molecule libraries.

As disclosed herein, an iterative in situ click chemistry approach wasutilized to synthesize biligand and triligand capture agents thatspecifically bind VEGF. The biligand capture agents exhibited improvedVEGF binding affinity and specificity versus their anchor ligand, andalso showed the ability to inhibit HUVEC proliferation mediated by VEGFbinding to VEGFR2. The triligand capture agents exhibited improvementsin VEGF binding affinity and specificity beyond that of the biligands,and also showed the ability to inhibit VEGF binding to VEGFR2. Three ofthe triligand capture agents were found to share a binding epitope withAvastin®. All the capture agents exhibited a high degree of stability inserum. Multimeric forms of the capture agents were also developed, withcertain of these multimeric capture agents displaying improved affinity,specificity, and/or efficacy.

Based on the results disclosed herein, the present application providesbiligand and triligand VEGF capture agents and multimers thereof, aswell as methods of using these capture agents to identify, detect,quantify, and separate VEGF and to diagnose, classify, and treat variousconditions associated with increased VEGF expression and/or activity.

VEGF Capture Agents:

Provided herein in certain embodiments are synthetic biligand VEGFcapture agents comprising two target-binding moieties. The firsttarget-binding moiety is referred to as an anchor ligand, and the secondis referred to as a secondary ligand.

Provided herein in certain embodiments are synthetic triligand VEGFcapture agents comprising three target-binding moieties. The firsttarget-binding moiety is referred to as an anchor ligand, the second isreferred to as a secondary ligand, and the third is referred to as atertiary ligand.

Provided herein in certain embodiments are multimeric forms of thebiligand and/or triligand VEGF capture agents disclosed herein. Incertain embodiments, these multimeric capture agents comprise dimers,trimers, or tetramers of the biligands and/or triligands disclosedherein. In certain embodiments, the multimeric capture agents arehomomultimers, meaning that all of the biligand and/or triligandcomponents of the multimer are identical. In other embodiments, themultimeric capture agents are heteromultimers, meaning that theycomprise two or more different biligands and/or triligands.

In certain embodiments, a target-binding moiety comprises one or morepolypeptides or peptides. In certain of these embodiments, atarget-binding moiety comprises one or more peptides comprising D-aminoacids, L-amino acids, and/or amino acids substituted with functionalgroups selected from the group consisting of substituted andunsubstituted alkyl, substituted and unsubstituted azido, substitutedand unsubstituted alkynyl, substituted and unsubstituted biotinyl,substituted and unsubstituted azidoalkyl, substituted and unsubstitutedpolyethyleneglycolyl, and substituted and unsubstituted 1,2,3-triazole.

In certain embodiments, the anchor ligand and secondary ligand in thebiligand and triligand capture agents provided herein are linked to oneanother via a covalent linkage. Similar, in certain embodiments thesecondary ligand and tertiary ligand in the triligand capture agentsprovided herein are linked to one another via a covalent linkage. Incertain of the above embodiments, the covalent linkage is an amide bondor a 1,4-disubstituted-1,2,3-triazole linkage as shown below:

In those embodiments where one or more target-binding moieties arelinked to one another via a 1,4-disubstituted-1,2,3-triazole linkage,the 1,4-disubstituted-1,2,3-triazole linkage may be formed bycopper-catalyzed azide/alkyne cycloaddition (CuAAC).

In certain embodiments, the anchor and secondary ligands and/or thesecondary and tertiary ligands are linked to one another by a Tz4linkage having the following structure:

In those embodiments wherein one or more of the anchor, secondary, andtertiary ligands are linked to one another via amide bonds, the amidebond may be formed by coupling a carboxylic acid group and an aminegroup in the presence of a coupling agent (e.g.,O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluroniumhexafluorophosphate (HATU), N-hydroxy-7-aza-benzotriazole (HOAt), ordiisopropylethylamine (DIEA) in DMF).

In certain embodiments of the biligand and triligand capture agentsprovided herein, the anchor ligand comprises the amino acid sequence setforth in SEQ ID NO:1. In other embodiments, the anchor ligand comprisesan amino acid sequence, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98 or 100% identical to the amino acid sequenceset forth in SEQ ID NO:1. In other embodiments, the anchor ligandcomprises a fragment of the amino acid sequence of SEQ ID NO:1. Incertain embodiments, this fragment contains 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17 or 18 amino acids. In other embodiments, thisfragment contains 5-18, 10-18, 5-15, 7-15, 9-15 or 3-16 amino acids.

In certain embodiments of the biligand and triligand capture agentsprovided herein, the anchor ligand has the structure set forth in FIG. 3or 4.

In certain embodiments of the biligand and triligand capture agentsprovided herein, the secondary ligand comprises a formula ofX2-X3-X4-X5-X6. In certain embodiments, X2 is selected from a positivelycharged D-amino acid, an aromatic D-amino acid and a neutral D-aminoacid. In other embodiments, X2 is selected from D-arginine,D-tryptophan, D-leucine, D-valine, glycine, D-proline, D-isoleucine andD-alanine. In other embodiments, X3 is selected from a neutral D-aminoacid, an aromatic D-amino acid or a positively charged amino acid. Incertain embodiments, X3 is selected from D-proline, D-phenylalanine,glycine, D-arginine, D-lysine, D-histidine, D-tryptophan and D-tyrosine.In other embodiments, X4 is selected from a neutral D-amino acid, apositively charged D-amino acid, an aromatic D-amino acid and a polarD-amino acid. In certain embodiments, X4 is selected from D-isoleucine,D-leucine, D-proline, D-alanine, D-arginine, D-phenylalanine,D-threonine and D-histidine. In other embodiments, X5 is selected from aneutral D-amino acid, a positively charged D-amino acid and a negativelycharged D-amino acid. In certain embodiments, X5 is selected fromD-isoleucine, glycine, D-valine, D-leucine, D-alanine, D-proline,D-lysine, D-glutamate, D-histidine and D-arginine. In other embodiments,X6 is selected from a positively charged D-amino acid, an aromaticD-amino acid, a neutral D-amino acid and a polar D-amino acid. Incertain embodiments, X6 is selected from D-arginine, D-lysine,D-tryptophan, D-tyrosine, D-proline, D-valine, glycine, D-isoleucine,D-alanine and D-glutamine.

In certain embodiments, X2 is selected from a positively charged D-aminoacid and an aromatic D-amino acid. In other embodiments, X2 is selectedfrom D-arginine and D-tryptophan. In other embodiments, X3 is selectedfrom a neutral D-amino acid and an aromatic D-amino acid. In certainembodiments, X3 is selected from D-proline, D-phenylalanine and glycine.In other embodiments, X4 is a neutral D-amino acid. In certainembodiments, X4 is selected from D-isoleucine, D-leucine, D-proline andD-alanine. In other embodiments, X5 is a neutral D-amino acid. Incertain embodiments, X5 is selected from D-isoleucine, glycine andD-valine. In other embodiments, X6 is a positively charged D-amino acid.In certain embodiments, X6 is selected from D-arginine and D-lysine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, D-valine, glycine andD-proline. In other embodiments, X3 is a positively charged amino acid.In certain embodiments, X3 is selected from D-arginine, D-lysine andD-histidine. In other embodiments, X4 is selected from a neutral D-aminoacid, a positively charged D-amino acid and an aromatic D-amino acid. Incertain embodiments, X4 is selected from D-proline, D-arginine andD-phenylalanine. In other embodiments, X5 is selected from a neutralD-amino acid and a positively charged D-amino acid. In certainembodiments, X5 is selected from D-leucine, D-isoleucine, D-alanine,D-proline and D-lysine. In other embodiments, X6 is selected from apositively charged D-amino acid, an aromatic D-amino acid and a neutralD-amino acid. In certain embodiments, X6 is selected from D-arginine,D-tryptophan, D-tyrosine, D-proline and D-valine.

In certain embodiments, X2 is a neutral D-amino acid. In otherembodiments, X2 is selected from D-leucine, glycine, D-proline,D-isoleucine and D-alanine. In other embodiments, X3 is an aromaticD-amino acid. In certain embodiments, X3 is selected from D-tryptophan,D-phenylalanine and D-tyrosine. In other embodiments, X4 is selectedfrom a positively charged D-amino acid, an aromatic D-amino acid and apolar D-amino acid. In certain embodiments, X4 is selected fromD-arginine, D-phenylalanine, D-threonine and D-histidine. In otherembodiments, X5 is selected from a neutral D-amino acid, a positivelycharged D-amino acid and a negatively charged D-amino acid. In certainembodiments, X5 is selected from glycine, D-alanine, D-proline,D-glutamate, D-histidine and D-arginine. In other embodiments, X6 isselected from a positively charged D-amino acid, an aromatic D-aminoacid, a neutral D-amino acid and a polar D-amino acid. In certainembodiments, X6 is selected from D-arginine, D-tryptophan, glycine,D-isoleucine, D-alanine and D-glutamine.

In other embodiments, the secondary ligand comprises an amino acidsequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20 and 21. In other embodiments, the secondary ligandcomprises an amino acid sequence, wherein one amino acid differs from anamino acid sequence selected from SEQ ID NOs:2, 3, 4, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20 and 21. In other embodiments, the secondaryligand comprises an amino acid sequence wherein the amino acid sequenceconsists of an amino acid sequence selected from SEQ ID NOs:2, 3, 4, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 and 21.

In certain embodiments of the biligand and triligand capture agentsprovided herein, the secondary ligand comprises the amino acid sequenceset forth in SEQ ID NOs:2, 3, or 4.

In certain embodiments of the biligand and triligand capture agentsprovided herein, the tertiary ligand comprises a formula ofX2-X3-X4-X5-X6. In certain embodiments, X2 is a positively chargedD-amino acid. In other embodiments, X2 is selected from D-histidine,D-arginine and D-lysine. In other embodiments, X3 is selected from apolar D-amino acid, a neutral D-amino acid and a negatively chargedamino acid. In certain embodiments, X3 is selected from D-threonine,D-asparagine, D-leucine, D-proline, D-isoleucine, D-alanine, andD-glutamate. In other embodiments, X4 is selected from a positivelycharged D-amino acid, an aromatic D-amino acid and a neutral D-aminoacid. In certain embodiments, X4 is selected from D-histidine, D-lysine,D-arginine, D-tryptophan, D-phenylalanine, D-proline, D-leucine andD-tyrosine. In other embodiments, X5 is selected from a neutral D-aminoacid, a positively charged D-amino acid, an aromatic D-amino acid and apolar D-amino acid. In certain embodiments, X5 is selected fromD-valine, D-proline, D-histidine, D-phenylalanine, D-tryptophan,D-asparagine, D-glutamine, D-serine and D-tyrosine. In otherembodiments, X6 is selected from a positively charged D-amino acid, anaromatic D-amino acid, a polar D-amino acid and a neutral D-amino acid.In certain embodiments, X6 is selected from D-arginine, D-tyrosine,D-asparagine, D-glutamine, D-leucine, D-proline, D-lysine andD-histidine.

In certain embodiments, X2 is an aromatic D-amino acid. In otherembodiments, X2 is selected from D-tyrosine, D-phenylalanine andD-tryptophan. In other embodiments, X3 is selected from a neutralD-amino acid and a positively charged amino acid. In certainembodiments, X3 is selected from D-proline, D-alanine, glycine,D-leucine, D-lysine, D-arginine and D-histidine. In other embodiments,X4 is selected from a positively charged D-amino acid, an aromaticD-amino acid, a negatively charged D-amino acid, a neutral D-amino acidand a polar D-amino acid. In certain embodiments, X4 is selected fromD-arginine, D-histidine, D-tryptophan, D-phenylalanine, D-glutamate,D-proline, D-serine and D-threonine. In other embodiments, X5 isselected from a neutral D-amino acid, a negatively charged D-amino acid,a positively charged D-amino acid, an aromatic D-amino acid and a polarD-amino acid. In certain embodiments, X5 is selected from D-proline,D-aspartate, D-lysine, D-arginine, D-tyrosine, D-histidine, D-alanine,D-valine, D-leucine and D-asparagine. In other embodiments, X6 isselected from a positively charged D-amino acid, a polar D-amino acid, aneutral D-amino acid, a negatively charged D-amino acid and an aromaticD-amino acid. In certain embodiments, X6 is selected from D-histidine,D-lysine, D-asparagine, D-threonine, D-glutamine, D-leucine,D-aspartate, D-serine, D-tyrosine, D-arginine, D-tryptophan, D-glutamateand D-valine.

In certain embodiments, X2 is negatively charged D-amino acid. In otherembodiments, X2 is selected from D-glutamate and D-aspartate. In otherembodiments, X3 is selected from a negatively charged D-amino acid, anaromatic D-amino acid, a positively charged amino acid and a polarD-amino acid. In certain embodiments, X3 is selected from D-glutamate,D-phenylalanine, D-tryptophan, D-histidine, D-lysine, D-asparagine andD-serine. In other embodiments, X4 is selected from a neutral D-aminoacid, a positively charged D-amino acid, a polar D-amino acid, anegatively charged D-amino acid and an aromatic D-amino acid. In certainembodiments, X4 is selected from D-isoleucine, D-proline, D-alanine,D-arginine, D-serine, D-aspartate, D-asparagine, D-proline,D-phenylalanine, D-tyrosine and D-histidine. In other embodiments, X5 isselected from a positively charged D-amino acid, an aromatic D-aminoacid and a neutral D-amino acid. In certain embodiments, X5 is selectedfrom D-arginine, D-tyrosine, glycine, D-tryptophan, D-lysine,D-histidine, D-alanine, D-asparagine and D-leucine. In otherembodiments, X6 is selected from a negatively charged D-amino acid, aneutral D-amino acid, an aromatic D-amino acid and a polar D-amino acid.In certain embodiments, X6 is selected from D-aspartate, D-proline,D-tryptophan, D-tyrosine, D-leucine, D-asparagine, D-serine andD-threonine.

In other embodiments, the tertiary ligand comprises an amino acidsequence selected from SEQ ID NOs:5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64. In other embodiments, the secondary ligand comprises an aminoacid sequence, wherein one amino acid differs from an amino acidsequence selected from SEQ ID NOs: 5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64. In other embodiments, the secondary ligand comprises an aminoacid sequence wherein the amino acid sequence consists of an amino acidsequence selected from SEQ ID NOs:5, 6, 7, 8, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 5, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63 and 64.

For all of the above embodiments, glycine is considered to be a memberof the genus of neutral D-amino acids, despite the achirality ofglycine.

In certain embodiments of the triligand capture agents provided herein,the tertiary ligand comprises the amino acid sequence set forth in SEQID NOs:5, 6, or 7.

In certain embodiments, the biligand capture agents provided herein havethe structure set forth in FIG. 6, 8, 9, or 10.

In certain embodiments, the triligand capture agents provided hereinhave the structure set forth in FIG. 11, 12, 13, or 14.

In certain embodiments, the capture agents provided herein are stableacross a range of reaction conditions and/or storage times. A captureagent that is “stable” as used herein maintains the ability tospecifically bind to a target protein and is at least partiallyresistant to proteolytic degradation.

In certain embodiments, the capture agents provided herein have ashelf-life of greater than six months, meaning that they are stable instorage for greater than six months. In certain of these embodiments,the capture agents have a shelf-life of one year or greater, two yearsor greater, or more than three years. In certain of these embodiments,the capture agents are stored as a lyophilized powder. In certainembodiments, the capture agents provided herein have a longer shelf-lifethan a biologic binding to the same target protein.

In certain embodiments, the capture agents provided herein are stable attemperatures ranging from about −80° to about 120° C. In certain ofthese embodiments, the capture agents are stable within a temperaturerange of −80° to −40° C.; −40° to −20° C.; −20° to 0° C.; 0° to 20° C.;20° to 40° C.; 40° to 60° C.; 60° to 80° C.; and/or 80° to 120° C. Incertain embodiments, the capture agents provided herein are stableacross a wider range of temperatures than a biologic binding to the sametarget protein, and/or remain stable at a specific temperature for alonger time period than a biologic binding to the same target protein.

In certain embodiments, the pH of a capture agent provided herein is inthe range of about 3.0 to about 12.0. In certain of these embodiments,the pH of the capture agent is in the range of about 5.0 to about 9.0.The pH of a capture agent may be adjusted to a physiologicallycompatible range using methods known in the art. For example, in certainembodiments the pH of the capture agent may be adjusted to the range ofabout 6.5 to about 8.5.

In certain embodiments, the capture agents provided herein are stable inblood serum for more than 12 hours. In certain of these embodiments, thecapture agents are stable in blood serum for more than 18 hours, morethan 24 hours, more than 36 hours, more than 48 hours, or more than 96hours. In certain embodiments, the capture agents provided herein arestable for a longer period of time in blood serum than a biologicbinding to the same target protein.

In certain embodiments, the capture agents provided herein may compriseone or more detection labels, including for example biotin,copper-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaceticacid(copper-DOTA), desferrioxamine B (DFO), a ligand for radiolabeling with⁶⁸Ga, or other radiolabeled products that may include gamma emitters,proton emitters, positron emitters, tritium, or covered tags detectableby other methods (i.e., gadolinium) among others.

In certain embodiments, the capture agents provided herein comprise oneor more detectable labels. In certain of these embodiments, the label iscopper-DOTA. In other embodiments, the detectable label is selected from⁶⁴Cu DOTA, ⁶⁸Ga DOTA, ¹⁸F, ⁶⁴Cu, ⁶⁸Ga, ⁸⁹Zr, ¹²⁴I, ⁸⁶Y, ^(94m)Tc,^(110m)In, ¹¹C and ⁷⁶Br. In other embodiments, the detectable label isselected from ¹²³I, ¹³¹I, ⁶⁷Ga, ¹¹¹In and ^(88m)Tc. In otherembodiments, the label is a fluorescent label.

In certain embodiments, the capture agents provided herein may bemodified to obtain a desired chemical or biological activity. Examplesof desired chemical or biological activities include, withoutlimitation, improved solubility, stability, bioavailability,detectability, or reactivity. Examples of specific modifications thatmay be introduced to a capture agent include, but are not limited to,cyclizing the capture agent through formation of a disulfide bond;modifying the capture agent with other functional groups or molecules.Similarly, a capture agent may be synthesized to bind to non-canonicalor non-biological epitopes on proteins, thereby increasing theirversatility. In certain embodiments, the capture agent may be modifiedby modifying the synthesis blocks of the target-binding moieties beforethe coupling reaction.

Provided herein in certain embodiments are pharmaceutical formulationscomprising one or more of the capture agents provided herein. In certainembodiments, these pharmaceutical formulations comprise one or morepharmaceutically acceptable carriers, excipients, or diluents. Thesecarriers, excipients, or diluents may be selected based on the intendeduse and/or route of administration of the formulation.

Provided herein in certain embodiments are kits comprising one or moreof the capture agents disclosed herein. In certain embodiments, thesekits may be used for identifying, detecting, quantifying, and/orseparating VEGF, and in certain of these embodiments the kits may beused in the diagnosis and/or staging of a condition associated withincreased VEGF expression and/or activity. In certain embodiments, a kitas provided herein comprises: (a) a substrate comprising an adsorbentthereon, wherein the adsorbent is suitable for binding VEGF, and (b) awashing solution or instructions for making a washing solution, whereinthe combination of the adsorbent and the washing solution allowsdetection of VEGF. In other embodiments, the kits provided herein may beused in the treatment of a condition associated with increased VEGFexpression and/or activity.

In certain embodiments, the kits provided herein may further compriseinstructions for suitable operational parameters in the form of a labelor a separate insert. For example, the kit may have standardinstructions informing a consumer/kit user how to wash the probe after asample of plasma or other tissue sample is contacted on the probe.

In certain embodiments, a kit as provided herein comprises (a) one ormore VEGF capture agents that specifically bind VEGF; and (b) adetection reagent. Such kits can be prepared from the materialsdescribed herein.

The kits provided herein may optionally comprise a standard or controlinformation, and/or a control amount of material, so that the testsample can be compared with the control information standard and/orcontrol amount to determine if the test amount of VEGF detected in asample is an amount consistent with a diagnosis of a particularcondition.

Methods of Using VEGF Capture Agents:

Provided herein in certain embodiments are methods of using the VEGFcapture agents disclosed herein to identify, detect, quantify, and/orseparate VEGF in a biological sample. The VEGF capture agents disclosedherein can serve as a drop-in replacement for monoclonal antibodies inbiochemical assays. Therefore, in certain embodiments the methodsprovided herein utilize an immunoassay, with the capture agent replacingan antibody or its equivalent. In certain embodiments, the immunoassaymay be a Western blot, pull-down assay, dot blot, or ELISA.

A biological sample for use in the methods provided herein may beselected from the group consisting of organs, tissue, bodily fluids, andcells. Where the biological sample is a bodily fluid, the fluid may beselected from the group consisting of blood, blood serum, plasma, urine,sputum, saliva, stool, spinal fluid, cerebral spinal fluid, lymph fluid,skin secretions, respiratory secretions, intestinal secretions,genitourinary tract secretions, tears, and milk.

Provided herein in certain embodiments are methods of identifying,detecting, quantifying, and/or localizing VEGF in vivo. In certain ofthese embodiments, the capture agents may be used as an imaging agent.In these embodiments, the capture agents may comprise one or moredetection labels as discussed above.

Provided herein in certain embodiments are methods of using the VEGFcapture agents disclosed herein to inhibit VEGF activity. In certain ofthese embodiments, the capture agents inhibit VEGF activity by blockingbinding of VEGF to VEGFR, thereby inhibiting VEGFR activity.Accordingly, further provided herein are methods of using the VEGFcapture agents disclosed herein to inhibit binding of VEGF to VEGFRand/or inhibit VEGFR activity. In certain of these embodiments, theVEGFR is VEGFR2.

Provided herein in certain embodiments are methods of using the VEGFcapture agents disclosed herein to diagnose and/or classify (e.g.,stage) a condition associated with increased VEGF expression and/oractivity, including for example various cancers. In certain embodiments,these methods comprise (a) obtaining a biological sample from a subject;(b) measuring the presence or absence of VEGF in the sample with theVEGF capture agent; (c) comparing the levels of VEGF to a predeterminedcontrol range for VEGF; and (d) diagnosing a condition associated withincreased VEGF expression based on the difference between VEGF levels inthe biological sample and the predetermined control.

In certain embodiments of the diagnosis and/or classification methodsprovided herein, the VEGF capture agents may be used to diagnose achange in health status in a subject, wherein the change in healthstatus is a predictor of a disease or event. In certain of theseembodiments, the methods may be utilized to predict the development of adisease or event in a subject who does not yet exhibit any symptoms ofthe disease or event. In certain embodiments, the change in healthstatus may be an increase in VEGF levels.

Provided herein in certain embodiments are methods of treating acondition associated with increased VEGF expression and/or activity in asubject in need thereof by administering a therapeutically effectiveamount of one or more of the capture agents or pharmaceuticalformulations disclosed herein. In certain of these embodiments, thecapture agent(s) may be linked to one or more additional therapeuticagents, including for example a chemotherapeutic agent. In preferredembodiments, the capture agent is administered as a pharmaceuticalcomposition. In certain embodiments, the condition being treated is adisease selected from the group consisting of cancer, proliferativeretinopathy, disease pathology of wet form AMD, or rheumatoid arthritis.

A capture agent or pharmaceutical formulation may be administered to apatient in need of treatment via any suitable route. Routes ofadministration may include, for example, parenteral administration(including subcutaneous, intramuscular, intravenous, by means of, forexample a drip patch). Further suitable routes of administration include(but are not limited to) oral, rectal, nasal, topical (including buccaland sublingual), infusion, vaginal, intradermal, intraperitoneally,intracranially, intrathecal and epidural administration oradministration via oral or nasal inhalation, by means of, for example anebulizer or inhaler, or by an implant.

A capture agent or pharmaceutical formulation may also be administeredvia microspheres, liposomes, other microparticulate delivery systems orsustained release formulations placed in certain tissues includingblood. Suitable examples of sustained release carriers includesemi-permeable polymer matrices in the form of shared articles, e.g.,suppositories or microcapsules. Examples of the techniques and protocolsmentioned above and other techniques and protocols which may be used inaccordance with the invention can be found in Remington's PharmaceuticalSciences, 18th edition, Gennaro, A. R., Lippincott Williams & Wilkins;20th edition (Dec. 15, 2000) ISBN 0-912734-04-3 and PharmaceuticalDosage Forms and Drug Delivery Systems; Ansel, N. C. et al. 7th EditionISBN 0-683305-72-7, the entire disclosures of which are hereinincorporated by reference.

Provided herein in certain embodiments is the use of the capture agentsdisclosed herein in the preparation of a medicament for treating acondition associated with increased VEGF expression and/or activity.

Methods of Making Capture Agents:

In certain embodiments, methods are provided for synthesizing a captureagent as provided herein. In certain embodiments, these methodscomprise:

-   -   a) preparing a synthesis block of a target-binding moiety, the        synthesis block comprising the target-binding moiety and at        least one reactive group that can form a desired linkage with        another synthesis block, wherein:        -   i) the linkage is selected from the group consisting of            amide linkage, 1,4-disubstituted 1,2,3-triazole linkage, and            1,5-disubstituted 1,2,3-triazole linkage; and        -   ii) all other active functional groups of the target-binding            moiety are protected to avoid undesired reactions; and    -   b) coupling the synthesis blocks of the target-binding moieties        to provide the capture agent.

The following examples are provided to better illustrate the claimedinvention and are not to be interpreted as limiting the scope of theinvention. To the extent that specific materials are mentioned, it ismerely for purposes of illustration and is not intended to limit theinvention. One skilled in the art may develop equivalent means orreactants without the exercise of inventive capacity and withoutdeparting from the scope of the invention.

EXAMPLES Example 1 Synthesis of VEGF Capture Agents

Three anti-VEGF biligand capture agents and four anti-VEGF triligandcapture agents were identified using an in situ click chemistryapproach.

Reagents.

Fmoc-D-X—OH (Fmoc, fluoren-9-ylmethoxycarbonyl) (X=Ala, Arg(Pbf) (Pbf,pentamethyldihydrobenzofuran-5-sulfonyl), Asn(Trt) (Trt, trityl),Asp(OtBu) (tBu, tert-butyl), Glu(OtBu), Gln(Trt), Gly, His(Trt), Ile,Leu, Lys(Boc) (Boc, ten-butyloxycarbonyl), Met, Phe, Pro, Ser(tBu),Thr(tBu), Trp(Boc), Tyr(tBu), and Val) (Anaspec; San Jose, Ga.). Aminoacid coupling reactions were performed in 1-methyl-2-pyrrolidinone (NMP,99%) withO-Benzotriazole-N,N,N′,N′-tetramethyl-uronium-hexafluoro-phosphate(HBTU; AAPPTec) and DIEA. For removal of Na-Fmoc protecting groups, asolution of 20% piperidine in NMP was used. For final deprotection ofthe peptide libraries, trifluoroacetic acid (TFA, 98% min. titration)and triisopropylsilane (TIS) were used. All solvents and reagents werepurchased from Sigma-Aldrich (St. Louis, Mo.).

Construction of Peptide Libraries.

Randomized OBOC libraries of pentapeptides were synthesized using aTitan 357 automatic synthesizer (AAPPTec) via standard split-mix methodson polyethylene glycol-grafted polystyrene beads (TentaGel S—NH₂, 90 pm,0.29 mmol/g, 2.86×10⁶ beads/g). In a typical library construction,non-natural D-stereoisomers were used at each position in the peptidesequence. For the coupling steps, a standard solid-phase peptidesynthesis method with Fmoc chemistry (Fields 1990) was used. The resinwas swelled in NMP for two hours in the collection vessel (CV). Thecoupling of Fmoc-methionine (4 equiv) was initiated by addition of 3.8equiv of HATU (ChemPep) and 12 equiv of DIEA. The coupling reaction wasrun for 30 minutes. Following the coupling step, the beads werethoroughly washed (4×NMP) and treated with 20% piperidine in NMP (5minutes followed by a 15 minute wash with a fresh aliquot ofdeprotection solution). The resin was thoroughly washed (4×NMP, 4×DCM)and divided into multiple equal-mass aliquots for the next cycle ofcoupling in the reaction vessel (RV). With the coupling and Fmocdeprotection completed, the resins were combined in the collectionvessel. The procedures were repeated until the desired length of peptidewas attained. The amino acid side chain protective groups were thenremoved by incubation in TFA (94%), water (3%), and TIS (3%) for twohours. The library resin was then washed thoroughly with dichloromethane(DCM; 5×), methanol (MeOH; 5×), water (5×), MeOH (5×), DCM (5×), anddiethyl ether (5×). The resulting resin was dried under vacuum andstored at 4° C.

Biligand Selection.

Selection was carried out using an in situ click chemistry techniquewhere the target protein acts as the catalyst that conjugates azide toalkyne candidate ligands (FIGS. 1 and 2; Agnew 2009). For the screen, a200-mg portion of the OBOC library, coupled with D-propargylglycine atthe N-terminus, was transferred into an 8-mL capacity Alltech vessel andpre-incubated in a blocking solution consisting of 0.05% NaN₃, 0.1%Tween 20, and 0.1% BSA in PBS buffer (pH 7.4), for two hours on a 360°rotator at 25° C. Separately, a 3 mL volume of 10 nM human VEGF165A(#ab56620; Abcam, MA) diluted in blocking solution was pre-incubatedwith the anchor ligand construct Biotin-PEG-VEPNCDIHVMWEWECFERL-Az4,where PEG=3× ethylene glycol linker, Az4=6-azido-L-norleucine,VEPNCDIHVMWEWECFERL=amino acid sequence of SEQ ID NO:1 (FIG. 3), andunderlining=disulfide constrained residues (FIG. 4) (Fairbrother 1998),for two hours on a 360° rotator at 25° C.

Anchor ligand was supplied at a 3000-fold molar excess of the protein.After draining the blocking solution from the OBOC library, thepre-incubated solution of 10 nM VEGF165A and anchor ligand was added tothe library resin and incubated for four hours on a 360° rotator at 25°C. The screen was washed with 3×5 mL of the blocking solution, and 3 mLof 1:10,000 AP-linked Streptavidin (#V5591; Promega) was incubated for45 minutes at 25° C. AP-linked streptavidin distinguished those beadswhich contain a biotin label, and therefore products of VEGF-templatedin situ click biligand conjugation. To eliminate non-specifically boundproteins, the screen was washed with 5×3 mL Blocking Solution, 5×3 mLWash 1 Buffer (25 mM Tris-Cl, 10 mM MgCl₂, 700 mM NaCl, pH 7.5), and 5×3mL Wash 2 Buffer (25 mM Tris-Cl, pH 7.5), and drained by vacuum.BCIP:NBT (#S3771; Promega), freshly prepared in Alkaline PhosphataseBuffer (100 mM Tris-HCl, pH 9.0, 150 mM NaCl, 1 mM MgCl₂), was used todevelop the screen. The most intensely colored purple beads (“hits”)were selected manually. Selected beads were treated with 7.5 M guanidinehydrochloride (pH 2.0) to remove bound proteins and then decolorizedwith NMP. Anti-screens were separately performed to eliminate beads thatdisplayed non-specific binding to the reagents used to visualize thescreen. Following this refinement, sequencing of authentic hits wasperformed with MALDI-TOF/TOF and a semi-automated algorithm (Lee 2010).Biligand hit sequences obtained from screening VEGF against acomprehensive library are shown in FIG. 66.

Candidate biligands against VEGF were analyzed and grouped by similarcharges and similar conserved motifs using a proprietary IntegratedDiagnostics bioinformatic clustering program. Candidate peptides weregrouped together based on physicochemical features (FIG. 5). Thisbioinformatic clustering method was used to rationally guide biligandcandidate selection, as non-randomly selected ligands occur on theextremes of the universe of physiochemical properties. Different classesof hits were also identified through this multidimensionalrepresentation (i.e., different clusters may sample different regions ofthe protein epitope).

Biligand candidates containing the 1,4-substituted-1,2,3-triazole werethen synthesized individually, and biological assays were performed todetermine the biligand with the largest improvement in VEGF bindingaffinity and specificity versus the anchor ligand.

The selected biligand capture agents comprised the anchor ligand of SEQID NO:1 and a secondary ligand comprising the amino acid sequence of SEQID NO:2 (rplir; “Biligand 1”), 3 (lfrew; “Biligand 2”), or 4 (fsrkte;“Biligand 3”). The structures of Biligands 1, 2, and 3 are set forth inFIGS. 8, 9, and 10, respectively.

Triligand selection. A 200-mg portion of the OBOC library, coupled withD-propargylglycine at the N-terminus, was transferred into an 8-mLcapacity Alltech vessel and pre-incubated in a blocking solutionconsisting of 0.05% NaN₃, 0.1% Tween 20, and 0.1% BSA in PBS buffer (pH7.4), for two hours on a 360° rotator at 25° C. Separately, a 3 mLvolume of 1 nM VEGF165A diluted in blocking solution was pre-incubatedwith the Biligand 2 constructBiotin-PEG-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Az4, where PEG=3× ethyleneglycol linker (FIG. 6), for two hours on a 360° rotator at 25° C.

The biligand was supplied at a 5000-fold molar excess of the protein.After draining the blocking solution from the OBOC library, thepre-incubated solution of 1 nM VEGF165A and biligand was then added tothe library resin and incubated for four hours on a 360° rotator at 25°C. Product screens and anti-screens implementing AP-linked Streptavidinwere performed as described above. Sequencing of authentic hits wasperformed with MALDI-TOF/TOF and a semi-automated algorithm (Lee 2010).Triligand hit sequences obtained from screening VEGF against acomprehensive library are shown in FIG. 69.

Hit sequences were analyzed using the proprietary Integrated Diagnosticsbioinformatic clustering algorithm that was used to guide triligandcandidate selection. Candidate peptides were grouped together based onphysicochemical features (FIG. 7).

Triligand candidates containing the 1,4-substituted-1,2,3-triazole werethen synthesized individually, and biological assays were performed todetermine the triligands with the largest improvements in VEGF bindingaffinity and specificity versus the biligand. Competitive assays werealso implemented to characterize inhibitory effects of triligands onVEGF binding to VEGFR2 and other species.

The selected triligand capture agents comprise Biligand 2 linked to atertiary ligand comprising the amino acid sequence of SEQ ID NO:5(frsvn; “Triligand 1”), 6 (eeird; “Triligand 2”), 7 (hthwl; “Triligand3”), or 8 (ewsrw; “Triligand 4”). The structures of Triligands 1-4 areset forth in FIGS. 11-14, respectively.

CNBr Cleavage of “Hit” Peptides from Single Beads.

A single bead was transferred to a microcentrifuge tube containing purewater (10 μL). After addition of CNBr (10 μL, 0.50 M in 0.2 N HClsolution) the reaction vessel was purged with argon and then placedunder microwave for one minute (Lee 2008). The resulting solution wasconcentrated under centrifugal vacuum for 2 hours at 45° C.

MALDI-MS and MS/MS Analysis of “Hit” Peptides Cleaved from Single Beads.

To each tube was added a-cyano-4-hydroxycinnamic acid CHCA (0.5 μL, 5mg/mL matrix solution in acetonitrile/water (70:30) containing 0.1% TFA(v/v)). The mixture solution was taken up to be spotted onto a 384-wellMALDI plate, which was allowed to stand for 15 minutes to dry naturally.Samples were then analyzed by matrix-assistedlaser-desorption/ionization (MALDI) time-of-flight (TOF) massspectrometry (MS) using a Bruker UltrafleXtreme™ TOF/TOF instrument(Bruker Daltonics; Bremen, Germany) operated in reflectron mode. MS/MSspectra were acquired for each sample in LIFT™ mode.

Example 2 Large-Scale Production of VEGF Capture Agents

Large scale production of the VEGF capture agents identified in Example1 was required for biological assays. Each triligand was prepared usinga combination of conventional and microwave-assisted Fmoc-based solidphase peptide synthesis (SPPS). Specifically, the differing tertiaryligands of each triligand were synthesized in parallel onto rink amideresin using an AAPPTEC Titan 357 peptide synthesizer. Each amino acidcoupling reaction incorporated 4 equiv of Fmoc-amino acid, 4 equiv ofHBTU, and 10 equiv of DIEA. Deprotection of the Fmoc group required 20%piperidine/NMP.

The rink amide bound tertiary ligands were transferred to a CEM Liberty1 microwave peptide synthesizer for the preparation of the anti-VEGFbiligand (X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4, where X is a pegylatedreporter tag (e.g., biotin-PEG, DOTA-PEG, etc.)). Each amino acid, PEGlinker, and reporter coupling reaction incorporated 4 equiv ofFmoc-amino acid, 4 equiv of HBTU, and 10 equiv of DIEA. Couplingconditions of the two Tz4 linkers were modified using 4 equiv ofFmoc-amino acid, 4 equiv of HATU and 10 equiv of DIEA. Deprotection ofthe Fmoc group required 20% piperidine/NMP. If no pegylated reporter wasrequired, the resin bound triligands were capped at the N-termini usingAc₂O/DIEA. Capture agents were purified by reversed phase HPLC using aC18 column and a linear gradient (Solvent A: H₂O+0.1% TFA, Solvent B:ACN+0.1% TFA).

Example 3 Binding Affinity Analysis

A direct, solid-phase microplate enzyme-linked immunosorbent assay(ELISA) was used to measure in vitro binding of capture agents toVEGF165 (#ab56620; Abcam, MA). Binding was also measured for the wholeIgG and Fab fragment (prepared by papain digestion) of the anti-VEGFmonoclonal antibody Bevacizumab (Avastin®). The ELISA was found to behighly sensitive and reliable for detecting binding over a range ofcapture agent concentrations. The equilibrium dissociation constant (KD)for the capture agents may be estimated as the concentrationcorresponding to half-maximal fluorescent emission. Assaying multiplecapture agents in parallel permits relative and absolute comparison ofin vitro binding.

NUNC MAXISORP™ microtiter plates were coated with 2 μg/mL VEGF165(#ab56620; Abcam, MA) in PBS pH 7.4 over 2 hour at 25° C. After washingeach well with PBS (3×), the plate was filled with 5% non-fat dry milkin TBS (25 mM Tris, 150 mM NaCl, pH 7.25) containing 0.1% (v/v) TritonX-100 and blocked for 2 hours at 25° C. The plate was washed with 1%non-fat dry milk in TBS containing 0.1% (v/v) Triton X-100 (3×), andthen serially diluted biotinylated capture agent in 1% non-fat dry milkin TBS containing 0.1% (v/v) Triton X-100 was incubated for 3 hours at25° C. After washing all microwells with TBS/0.1% (v/v) Triton X-100(5×), 0.1 μg/mL Streptavidin Poly-HRP conjugate (Pierce, Ill.) inTBS/0.1% (v/v) Triton X-100 was incubated for 30 minutes at 25° C. Theplate was aspirated and washed with TBS/0.1% (v/v) Triton X-100 (5×),followed by TBS (5×), and then developed by adding QuantaRed™ EnhancedChemifluorescent HRP Substrate. Using an excitation wavelength of 535nm, fluorescent emission at 595 nm was recorded by Beckman CoulterDTX880 photometer (Brea, Calif.) as a function of capture agentconcentration. The titration curves were fit using a four-parameterregression curve fitting program (Origin 8.5, Northampton, Mass.).

The affinity of Triligands 2 and 3, Biligand 2, and the anchor ligand ofthese capture agents are shown in FIG. 15. The affinity of Biligand 1and Triligands 1 and 4 are further shown in FIGS. 67 and 70,respectively. As a detection agent, Biligand 2 showed five-foldimprovement in its affinity for VEGF relative to the anchor ligandalone, while the best triligands showed an additional affinity gain (2-3fold, KDF≈15 nM). These results suggest that the capture agent selectionprocess inherently develops affinity. The affinities of Avastin® andAvastin® Fab were measured as KDF≈0.2 nM and KDF≈4.5 nM, respectively,and it appears that the decreased avidity of Avastin® Fab is manifestedas loss in affinity in this experiment. In the same way that Avastin®divalency confers affinity and avidity over the Fab fragment, a dimerictriligand capture agent provides additional affinity gains.

Example 4 Binding Specificity Analysis

A pull-down assay was used to assess capture agent specificity for VEGFby measuring the ability of the capture agents to purify VEGF165 frombuffer or complex media such as human serum. Capture agents wereimmobilized on streptavidin-functionalized magnetic beads, and theresultant resins were panned with VEGF165-spiked serum or buffer.

Pull-down detection of VEGF165 was performed using a modifiedimmunoprecipitation technique that incorporated capture agents ratherthan antibody. First, biotinylated capture agent (400 nM; 0.1% DMSO,v/v) was incubated with 1 μg/mL VEGF165 in 2 mL TBS at 4° C. overnight.Separately, biotinylated capture agent (400 nM; 0.1% DMSO, v/v) wasincubated with 1 μg/mL VEGF165 in 2 mL of 25% (v/v) human AB male serum(#HS-20, Omega Scientific, Tarzana, Calif.) under the same conditions(4° C., overnight). A vehicle-only control (0.1% DMSO, v/v) accompaniedeach sample.

Proteins were captured by BSA-blocked Dynabeads® M-280 Streptavidin(Invitrogen, #112-05D) under rotation at 4° C. for 4 hours (100 μL of50% slurry per pull-down condition). Beads were separated from the serumor buffer matrix by application of the DynaMag™-Spin magnet (Invitrogen,#123-20D), and captured proteins were eluted from the beads in 30 μL ofreducing Laemmli buffer. Eluted samples were subjected to 12% SDS-PAGEseparation at 200 V for 30 minutes in 1×TGS (25 mM Tris, 192 mM Glycine,0.1% SDS (w/v), pH 8.3). Samples were subsequently electrophoreticallytransferred to a nitrocellulose membrane in 25 mM Tris, 192 mM Glycine,pH 8.3, containing 20% (v/v) methanol (Bio-Rad Laboratories, Hercules,Calif.) at 100 V for 45 minutes. Following transfer, the nitrocellulosemembrane was blocked at 4° C. for 2 hours in 5% non-fat dry milk in TBS.The membrane was then washed with TBS (3×), and 1 μg/mL mouse anti-humanVEGF165 antibody [6B7] (#ab69479; Abcam, MA) in 0.5% non-fat dry milk inTBS was incubated at 4° C. overnight. After washing with TBS containing0.02% Tween20 (v/v) (5×), 0.2 μg/mL HRP-conjugated goat polyclonalsecondary antibody to mouse IgG (H+L) (#ab6789; Abcam, MA) in 0.5%non-fat dry milk in TBS was added to the membrane (4° C., 1 hourincubation). After washing with TBS containing 0.02% Tween20 (v/v) (5×),followed by TBS (5×), the membrane was developed with SuperSignal WestPico Chemiluminescent Enhancer and Substrate Solutions (Pierce, Ill.)and then immediately exposed to HyBlot CL AR film. Separately, aduplicate 12% gel was visualized for total protein content by silverstain (Bio-Rad Laboratories, Hercules, Calif.) to estimate specificityof capture agents in comparison to the Western result.

Results of pull-down assays are set forth in FIGS. 16, 68, 71, and 73.Probing the elutions via Western blot with a VEGF antibody confirms theincrease in capture efficiency as the combined affinity/specificitymetrics of the capture agent are increased by translating from anchor tobiligand to triligand. Analysis of the total immunoprecipitated proteinby SDS-PAGE showed tolerable to low non-selective binding for allcapture agents, and correlates well with the capture efficiency forVEGF. VEGF detection from human serum was observed only after the anchorligand was developed into biligand and then triligand capture agents.Triligand 2 captures equivalent amounts of VEGF in buffer and serum(lanes B vs. S), indicating the highest attainable capture agentspecificity, and compares well with the Avastin® result.

These results suggest that the capture agent selection process not onlydevelops affinity, but also inherently develops specificity. The resultsalso suggest that triligands of equivalent affinity are not necessarilyequivalent in specificity (compare Triligands 2 and 3); therefore, bothaffinity and specificity are critical performance parameters of captureagents that can mature independently.

Example 5 Serum Stability

Proteolytic stability is an important factor for the use of peptides inin vivo applications and for serum protein diagnostics. Most naturalpeptides have to be modified to prevent enzymatic degradation. Severalapproaches including the use of D-amino acids, non-natural amino acids,and cyclization have been used to improve capture agent stability.

Stability was studied by mixing 200 μg capture agent in TBS containing25% (v/v) human AB male serum (HS-20, Omega Scientific, Tarzana, Calif.)in 800 μL total volume (see, e.g., Pakkala 2007). Peptides wereincubated at 37° C., and 100 μL aliquots were taken at 0 minutes, 30minutes, and then after every hour up to 4 hours. A final aliquot wastaken after 24 hours. The peptide was separated from plasma proteins ona Microcon centrifugal filter device (Microcon YM-10, MWCO=10 kDa,Millipore, Bedford, Mass.) by centrifugation at 12,000 rpm using aBeckman Coulter refrigerated microcentrifuge (Brea, Calif.) for 20 min.The filtrates were examined by analytical HPLC (C18 column, lineargradient of 0→100% B over 60 min, where A=H₂O+0.1% TFA and B=ACN+0.1%TFA), followed by Bruker UltrafleXtreme MALDI mass spectrometry.

Two control assays were performed in parallel and subjected to the sameconditions as above: 1) Biligand 2 in TBS, and 2) TBS containing 25%(v/v) human AB male serum.

The capture agent was still intact after incubation with either humanserum or buffer for 24 hours at 37° C. (FIG. 17), suggesting that thecapture agent is stable to proteolytic degradation in human serum formore than 24 hours at physiological temperature and buffer. The resultsindicate that cyclization is an efficient and simple approach to improveresistance to proteolytic digestion for sequence segments containing(natural) L-amino acids, and that D-amino acids and non-natural aminoacids are intrinsically stable elements. This approach, without anysequence modifications, could be useful for designing peptides for invivo studies.

Example 6 Inhibition of HUVEC Proliferation

Human umbilical vein endothelial cells (HUVECs) constitutively secreteVEGF, which binds to VEGFR2 in an autocrine fashion. Avastin® bindsdirectly to VEGF and blocks formation of the VEGF-VEGFR2 complex,thereby attenuating proliferation by blocking receptor signaling.Biligand capture agents were evaluated for their ability to inhibitHUVEC proliferation.

HUVECs were cultured in M199 medium (pH 7.4) in 5% CO₂ at 37° C. for 18hours. Test compound and/or vehicle were incubated with cells(1.1×10⁵/mL) in the presence of heparin (10 μg/mL) and 0.5% FBS at 37°C. for 48 hours. Capture agents were screened at 10, 1, 0.1, 0.01 and0.001 μM and in duplicate. Avastin® was screened at 100, 10, 1, 0.1 and0.01 nM and in duplicate. VEGF165 (agonist, EC₅₀=0.079 nM) and SU5416(antagonist, IC₅₀=48 nM) were assayed as standard references.Subsequently, the reagent Calcein AM dye (20 μg/ml) was added for anadditional 50 minute incubation period. Fluorescence intensity was readon SpectroFluor Plus plate reader.

Response curves illustrating percent inhibition versus test compoundconcentration are set forth in FIG. 18. Test compound-inducedstimulation of cell proliferation by 50% or more, relative to 1 nMVEGF165 control response, indicates significant agonist activity, whiletest compound-induced suppression of 0.2 nM VEGF165-induced cellproliferation by 50% or more indicates significant antagonist activity.Results are shown in FIG. 18. Tabulated IC₅₀ values confirmAvastin®-mediated antagonism (IC₅₀=0.687 nM) as a positive control.

Binding of capture agents to soluble VEGF prevents ligation to VEGFR2 onthe cell surface and attenuates proliferation by blocking signalingthrough the receptor.

Example 7 Pharmacokinetics

A preliminary pharmacokinetic assessment of Biligand 2 was performedfollowing intravenous (IV) and intraperitoneal (IP) dosing to mice.

HPLC-MS Optimization.

Test compound solutions were prepared as specified in Tables 1 and 2 andinfused into the TSQ Quantum source via syringe pump at a constant rate.Full scan MS analysis was conducted and total ion current chromatogramsand corresponding mass spectra were generated for the test compound inboth positive and negative ionization modes. The precursor ions forMS/MS were selected from either the positive or the negative massspectrum, as a function of the respective ion abundance. In addition,product ion MS/MS analysis was performed in order to determine theappropriate selected fragmentation reaction for use in quantitativeanalysis. The final reaction monitoring parameters were chosen tomaximize the ability to quantify the test compound when present within acomplex mixture of components. Following identification of the specificSRM transition to be used for each test compound, the detectionparameters were optimized using the automated protocol in the TSQQuantum Compound Optimization workspace. Finally, the chromatographicconditions to be used for LC-MS analysis were identified by injectionand separation of the analyte on a suitable LC column and adjustment ofthe gradient conditions as necessary.

TABLE 1 General procedures Assay Sample Preparation Bibliography HPLC-MSoptimization Watt 2000 Linearity (plasma, Calibration curve;acetonitrile Watt 2000 mouse) precipitation Quantitative Calibrationcurve; acetonitrile Watt 2000 bioanalysis (plasma, precipitation mouse)

TABLE 1 Experimental conditions Detection Assay Test Compound MethodsHPLC-MS 1000 ng/mL HPLC-MS and optimization HPLC-MS/MS Linearity(plasma, 0, 1, 2.5, 5, 10, 50, 250, HPLC-MS/MS mouse) 1000, 2500, 5000ng/mL HPLC-MS/MS Quantitative Unknown in plasma samples HPLC-MS/MSbioanalysis (plasma, mouse)

Linearity in Plasma.

Aliquots of plasma were spiked with the test compound at the specifiedconcentrations. The spiked samples were processed using acetonitrileprecipitation and analyzed by HPLC-MS or HPLC-MS/MS. A calibration curveof peak area versus concentration was constructed. The reportable linearrange of the assay was determined, along with the lower limit ofquantitation (LLQ).

Quantitative Bioanalysis (Plasma).

The plasma samples were processed using acetonitrile precipitation andanalyzed by HPLC-MS/MS. A plasma calibration curve was generated.Aliquots of drug-free plasma were spiked with the test compound at thespecified concentration levels. The spiked plasma samples were processedtogether with the unknown plasma samples using the same procedure. Theprocessed plasma samples were stored at −20° C. until the HPLC-MS/MSanalysis, at which time peak areas were recorded, and the concentrationsof the test compound in the unknown plasma samples were determined usingthe respective calibration curve. The reportable linear range of theassay was determined, along with the lower limit of quantitation (LLQ).

Formulation.

The solubility of the test compound is first evaluated inphosphate-buffered saline, pH 7.4 (PBS) by visual inspection. PBS isused as the vehicle if the compound is soluble at the targetconcentrations. Other vehicles that are compatible with IV dosing may beevaluated if the compound is not fully soluble in PBS. Such vehiclesinclude DMSO, Solutol® HS 15, and Cremophor EL among others. For IPdosing, DMSO/Solutol® HS 15/PBS (5/5/90, v/v/v), or DMSO/1%methylcellulose (5/95, v/v) may be used as the vehicle if the testcompound is not fully soluble in PBS. Customized formulations can beaccommodated.

Plasma Sample Collection from Mice (Parallel Sampling).

In vivo pharmacokinetic characterization was performed as specified inTables 3-5. Animals were sedated under general inhalant anesthesia (3%isoflurane) for blood collection by cardiac puncture. Each mouse wassubject to one blood draw. Blood aliquots (300-400 μL) were collected intubes coated with lithium heparin, mixed gently, then kept on ice andcentrifuged at 2,500×g for 15 minutes at 4° C., within 1 hour ofcollection. The plasma was then harvested and kept frozen at −20° C.until further processing.

TABLE 3 General procedures, in vivo PK Assay Source Dose TechniqueBibliography PK in-life (mouse, Male mice 1 mg/kg Tail vein Hosten 2008IV, parallel CD-1, injection/ blood sampling) weighing collection 20-30g PK in-life (mouse, Male mice 5 mg/kg Gastric Hosten 2008 IP, parallelCD-1, gavage/ blood sampling) weighing collection 20-30 g

TABLE 4 Experimental conditions, in vivo PK Assay Sampling Time PointsPK in-life (mouse, IV, parallel  3, 10, 30, 60, 120, 240, 360, 1440 minsampling) PK in-life (mouse, IP, parallel 10, 30, 60, 120, 240, 360,480, 1400 min sampling)

TABLE 5 Animal dosing design, in vivo PK (non-cannulated, non-fastedmice) Group Experiment* 1 Biligand 2, IV, n = 3 mice per time point (24animals total) 2 Biligand 2, IV, n = 3 mice per time point (24 animalstotal) 3 Control animals (for drug-free blood), n = 6 mice

Plots of plasma concentration of compound versus time were constructed.The fundamental pharmacokinetic parameters of compound after IP and IVdosing (AUClast, AUCINF, Tv2, CI, VZ, Vss, Tmax, and Cmax) were obtainedfrom the non-compartmental analysis (NCA) of the plasma data usingWinNonlin. The bioavailability was calculated, if applicable.Noncompartmental analysis does not require the assumption of a specificcompartmental model for either drug or metabolite. NCA allows theapplication of the trapezoidal rule for measurements of the area under aplasma concentration-time curve (Gabrielsson, J. and Weiner, D.Pharmacokinetic and Pharmacodynamic Data Analysis: Concepts andApplications. Swedish Pharmaceutical Press. 1997).

Graphs of the half-life for each route of administration are shown inFIG. 19, and the calculated PK parameters are summarized in Tables 6 and7. As expected for peptides, the compound is cleared rapidly upon IVadministration (T_(1/2)=7 min). Interestingly, there is a significantdifference between the IV half-life and the IP half-life (T_(1/2)=154min). There also appears to be two phases to the half-life for IPadministration. These results suggest that IP is the superior route ofadministration.

TABLE 6 In vivo mouse PK analysis, IV administration of Bilig2-Itrew(Biligand 2) Dose T½ CL Vz Vss AUClast AUCINF Terminal ROA (mg/kg) (min)(mL/min/kg) (mL/kg) (mL/kg) (min*ng/mL) (min*ng/mL) Points IV 1 7 15 158160 62760 66512 3

TABLE 7 In vivo mouse PK analysis, IP administration of Bilig2-Itrew(Biligand 2) Dose T½ Bioavailability Tmax Cmax AUClast AUCINF TerminalROA (mg/kg) (min) (%) (min) (ng/mL) (min*ng/mL) (min*ng/mL) Points IP 5154 41 10 3207 130030 145410 2

Example 8 Inhibition of VEGF Binding to VEGFR2

To measure the ability of capture agents to inhibit human VEGF165binding to VEGFR2 (KDR), ELISA plates were coated with 10 μg/mL rabbitF(ab′)2 to human IgG Fc (#309-006-008; Jackson ImmunoResearch, WestGrove, Pa.) in 50 mM carbonate buffer, pH 9.6, at 25° C. for 2 hours andblocked overnight at 4° C. with 5% non-fat dry milk in TBS (25 mM Tris,150 mM NaCl, pH 7.25) containing 0.1% (v/v) Triton X-100. Recombinanthuman VEGFR2 (KDR), Fc chimera (#357-KD, 10 μg/mL; R&D Systems,Minneapolis, Minn.) in TBS containing 0.1% (v/v) Triton X-100 wasincubated on the plate for 1 hour at 25° C. Three-fold serial dilutionsof capture agent or Avastin® Fab were incubated with 10 nM biotinylatedVEGF165 (biotinylated using #21435 EZ-Link Sulfo-NHS-LC-Biotinylationkit, Pierce, Ill.) in 1% non-fat dry milk in TBS containing 0.1% (v/v)Triton X-100 for 2 hours in tubes. The solutions from the tubes werethen transferred to the ELISA plates and incubated for 5 minutes. Boundbiotinylated VEGF165 was detected using 0.2 μg/mL horseradishperoxidase-labeled streptavidin (#ab7403; Abcam, MA) prepared in TBScontaining 0.1% (v/v) Triton X-100 and then developed by addingQuantaRed™ Enhanced Chemifluorescent HRP Substrate. Using an excitationwavelength of 535 nm, fluorescent emission at 595 nm was recorded byBeckman Coulter DTX880 photometer (Brea, Calif.) as a function ofcapture agent concentration. The titration curves were fit using afour-parameter regression curve fitting program (Origin 8.5,Northampton, Mass.). Concentrations of peptides corresponding to themidpoint absorbance of the titration curve were calculated and used asthe IC₅₀ values.

The in vitro blocking potential of Triligands 2 and 3, Biligand 2, andthe anchor ligand of these capture agents is shown in FIG. 20. The invitro blocking potential of Triligands 1 and 4 are further shown in FIG.72. Neither the anchor nor Biligand 2 blocked receptor binding at theconcentrations tested (<50 μM). Therefore, the tertiary ligand componentof the triligand capture agent appears to contribute significantly tothe blocking activity, while the anchor and secondary ligand componentsprovide enhancements in affinity and specificity. Three classes oftriligand capture agents identified in this application (Triligands 2-4)were each found to each have binding sites that overlap significantlywith the receptor-binding site. The largest in vitro blocking effect wasobserved for triligand 2 (IC₅₀=2 μM), which is within 100-fold of theIC₅₀ measured for Avastin® Fab. Even a partial blockade of VEGF may besufficient to block in vivo tumor angiogenesis (Liang 2006).

Example 9 Inhibition of VEGF Binding to Avastin® Fab

A solid-phase competitive assay was used to quantify capture agentbinding to the receptor interaction surface on VEGF in the presence ofAvastin® Fab. Since the triligand capture agents and Avastin® Fab sharesimilar binding affinities, concentration-dependent competition wouldconfirm that they share binding epitopes. NUNC MAXISORP™ microtiterplates were coated with 10 μg/mL Avastin® Fab in 50 mM carbonate buffer,pH 9.6, at 25° C. for 2 hours and blocked overnight at 4° C. with 5%non-fat dry milk in TBS (25 mM Tris, 150 mM NaCl, pH 7.25) containing0.1% (v/v) Triton X-100. Two-fold serial dilutions of capture agent wereincubated with 10 nM biotinylated VEGF165 in 1% non-fat dry milk in TBScontaining 0.1% (v/v) Triton X-100 for 1 hour on the Fab-immobilizedplate. Bound biotinylated VEGF165 was detected using 0.2 μg/mLhorseradish peroxidase-labeled streptavidin (#ab7403; Abcam, MA)prepared in TBS containing 0.1% (v/v) Triton X-100 and then developed byadding QuantaRed™ Enhanced Chemifluorescent HRP Substrate. Using anexcitation wavelength of 535 nm, fluorescent emission at 595 nm wasrecorded by Beckman Coulter DTX880 photometer (Brea, Calif.) as afunction of capture agent concentration. The titration curves were fitusing a four-parameter regression curve fitting program (Origin 8.5,Northampton, Mass.). Concentrations of peptides corresponding to themidpoint absorbance of the titration curve were calculated and used asthe IC₅₀ values.

In vitro competition between Avastin® Fab and capture agents is shown inFIG. 21. VEGF blocking was observed with Triligand 2 (IC₅₀=0.4 μM) andTriligands 1 and 3 (IC₅₀=2 μM), suggesting that the triligand-bindingepitopes on VEGF overlap with the epitope for Avastin® Fab. Biligand 2also displayed concentration-dependent competition but was not assignificant as the triligand capture agents, suggesting again that thetertiary ligand component appears to confer specific binding propertiesthat result in greater coverage of the epitope.

Example 10 Plasma Protein Binding

Equilibrium dialysis techniques were used to separate the fraction ofunbound test compound from the fraction that is bound to protein.

Assays were carried out in a 96-well format in a dialysis blockconstructed from Teflon. The protein matrix was spiked with the testcompound at 10 μM (n=2) with a final DMSO concentration of 1% (v/v). Thedialysate compartment was loaded with 150 μL phosphate buffer (pH 7.5)and the sample side was loaded with equal volume of the spiked proteinmatrix. The dialysis plate was then sealed and incubated at 37° C.overnight (18±2 hours). After the incubation, samples were taken fromeach compartment, diluted with the phosphate buffer followed by additionof acetonitrile and centrifugation. The supernatants were then used forHPLC-MS/MS analysis. A control sample (n=2) was prepared from the spikedprotein matrix in the same manner as the assay samples (withoutdialysis). This control sample served as the basis for the recoverydetermination. Samples were analyzed by HPLC-MS/MS using selectedreaction monitoring. The HPLC conditions consisted of a binary LC pumpwith autosampler, a C18 column (2×20 mm), and gradient elution. Thepercent bound to proteins and the recovery were calculated as follows:

${{Protein}\mspace{14mu} {binding}\mspace{14mu} (\%)} = {\frac{\left( \text{?} \right) \times \text{?}}{{\left( \text{?} \right) \times \text{?}} + \text{?}} \times 100}$${{Recovery}\mspace{14mu} (\%)} = {\frac{\left( {{\text{?} \times \text{?}} + {\text{?} \times \text{?}}} \right)}{\text{?} \times \text{?}} \times 100}$?indicates text missing or illegible when filed                    

where Area_(pe) is the peak area of analyte in the protein matrix atequilibrium, Area_(be) is the peak area of analyte in the Assay Bufferat equilibrium, V_(pe) is the volume of the protein matrix atequilibrium, VP; is the initial volume of the protein matrix, andArea_(cs) is the peak area of analyte in control sample. The recoverydetermination served as an indicator of reliability of the calculatedprotein binding value.

Most successful drugs have a plasma binding component. Low plasmaprotein binding illustrates high specificity, while higher degrees ofplasma protein binding predict that a compound will display longercirculation times and potentially increased access to the target at theexpense of poorer specificity. Analysis of the plasma protein bindingresults indicates that Biligand 2 (Bilig2-lfrew) displays low plasmaprotein binding (FIG. 22), while Biligand 3 (Bilig3-fsrkte) exhibitedhigher levels of plasma protein binding. Plasma protein binding bycapture agents compares well against octreotide (a peptide therapeutic)and warfarin (a small molecule drug). The trends in plasma proteinbinding for capture agents mirror the trends in pull-down assay andWestern blot results (Example 4). The percent protein recovery was highfor all capture agents, suggesting there is no sample degradation duringthe course of the assay.

Example 11 Stability in Human Plasma and Mouse Liver Microsomes

Capture agent stability in human plasma was quantified at multipletimepoints by HPLC-MS/MS analysis.

Human plasma was pre-warmed at 37° C. water bath for 5 minutes, followedby addition of 5 μM test compound with a final DMSO concentration of0.5% (v/v). The incubation was performed in a 37° C. water bath for 0,15, 30, 45, and 60 minutes. At each time point, an aliquot of theincubation mixture was transferred to acetonitrile. Samples were thenmixed and centrifuged. Supernatants were used for HPLC-MS/MS analysis.Samples were analyzed by HPLC-MS/MS using selected reaction monitoring.The HPLC system consisted of a binary LC pump with autosampler, a C-18column, and a gradient. Peak areas corresponding to the test compoundwere recorded. The compound remaining (%) was calculated by comparingthe peak area at each time point to time zero.

The test compound was pre-incubated with pooled mouse liver microsomes(male CD-1, 0.3 mg/mL) in phosphate buffer (pH 7.4) for 5 minutes in a37° C. shaking waterbath. Concentration of the test compound was 1 μMwith 0.01% DMSO, 0.25% acetonitrile and 0.25% methanol. The reaction wasinitiated by adding NADPH— generating system (1.3 mM NADP, 3.3 mM G6P,and 0.4 U/mL G6PDHase) and incubated for 0, 15, 30, 45, and 60 minutes.The reaction was stopped by transferring the incubation mixture to equalvolume of acetonitrile/methanol (1/1, v/v). Samples were then mixed andcentrifuged. Supernatants were used for HPLC-MS/MS analysis. Sampleswere analyzed by HPLC-MS/MS using selected reaction monitoring. The HPLCsystem consisted of a binary LC pump with autosampler, a C-18 column,and a gradient. Peak areas corresponding to the test compound wererecorded. The compound remaining was calculated by comparing the peakarea at each time point to time zero. The half-life was calculated fromthe slope of the initial linear range of the logarithmic curve ofcompound remaining (%) vs. time, assuming first order kinetics. Inaddition, the intrinsic clearance was calculated from the half-life.

All capture agents tested were found to be stable in human plasma andmouse liver microsomes at 37° C. over the assay period of 60 minutes(FIG. 23). Capture agent stability is similar to that of peptides (e.g.,octreotide) and surpasses that of some small molecules (e.g.,propantheline, propanolol). This is an indication that capture agentsmay be administered in vivo without anticipation of degradation.

Example 12 Tetrameric Variant of Triligand Capture Agent

A tetrameric variant of Triligand 2 was prepared via non-covalentassembly on a streptavidin scaffold. Streptavidin is a tetramericprotein produced by Streptomyces avidinii that binds to biotin with anextremely high affinity (KD˜1×10⁻¹⁵ M) and specificity and represents anideal scaffold to enhance the functional potential of the triligandcapture agent. A single streptavidin tetramer may bind to four differentbiotin molecules, or, as set forth below, to four biotinylated captureagents.

To prepare the triligand tetramer, 4.1 μL of 4.19 mM Triligand 2 stocksolution (4.5 equiv) in DMSO and 200 μL of 19 μM streptavidin tetramer(1 equiv; Promega, #Z7041) in phosphate-buffered saline (PBS; pH 7.4)were incubated on a rotator at 4° C. for 60 minutes (FIG. 24). To removeconjugates containing unoccupied biotin binding sites (i.e., conjugateswith less than four triligands per Sa tetramer), Pierce Biotin Agarose(#20218) was subsequently added and this mixture was incubated at 4° C.for 60 minutes on the rotator. This treatment was followed by additionof 2 mL of Dynabeads® M-280 Streptavidin (10 mg/mL slurry, 650-900pmol/mg biotin binding capacity; Invitrogen, #112-06D) and incubationfor 30 minutes on the rotator at 4° C. to remove all excess biotinylatedmolecules. Finally, the Sa-Dynabeads were pelleted by applying amagnetic field (DynaMag™-Spin; Invitrogen, #123-20D) to obtain thepurified triligand tetramer.

Variants of the triligand tetramer described above may be generated thatincorporate one or more covalently linked probes or functional groups(e.g., DOTA, fluorophore, enzymatic tag, additional biotin molecules).Exemplary methods of preparing a DOTA-labeled Triligand 2 tetramer areshown in FIGS. 25 and 27. An exemplary method of preparing anHRP-labeled Triligand 2 tetramer is shown in FIG. 50. These methods aregenerally applicable to any biotin-conjugated capture agent combinedwith any functional group of interest.

The method set forth in FIG. 25 takes advantage of a bifunctionalTriligand 2 presenting both covalent C-terminal biotin and N-terminalDOTA labels within a single molecule (FIG. 26). The labeled Triligand 2tetramer is prepared by non-covalent assembly on a streptavidin scaffoldas described above for the non-labeled triligand.

The method set forth in FIG. 27 utilizes an engineered variant ofstreptavidin expressing a C-terminal cysteine residue (Kwong 2009). ThisC-terminal cysteine residue may be used to install various labelinggroups (e.g., DOTA, biotin, or fluorophore) on the triligand tetramervia thiol-reactive coupling (see, e.g., US Patent Publication No.2011/0039717). In FIG. 27, the C-terminal cysteine is used to generate aDOTA-labeled streptavidin tetramer. In this example, the streptavidintetramer is reacted with Maleimido-mono-amide-DOTA (B-272; Macrocyclics,TX). After dialysis to remove excess DOTA label, biotin-labeledTriligand 2 (FIG. 28) is linked to the tetramer as described above.

The method set forth in FIG. 50 results in a Triligand 2 tetramer linkedto horseradish peroxidase.

Isolated triligand tetramers will be characterized by SDS-PAGE (7.5%gel). To retain the intact tetramer, samples will be prepared undernon-reducing conditions and without boiling. The tetrameric triligandcapture agent will be evaluated for affinity and specificity towardsVEGF, and will also be evaluated for biological activity in vitro (e.g.,displacement of VEGF from VEGFR and/or antagonism resulting in decreasedcell growth) and in vivo (e.g., reduction of angiogenesis).

Example 13 Other Multimeric Variants of Capture Agents

Multimeric variants (e.g., dimers, trimers, and tetramers) of thebiligands and triligands disclosed herein will be synthesized by variousmethods.

Homomultimeric biligand capture agents may be synthesized using themethod shown in FIG. 29 for Biligand 2. A multimeric variant will besynthesized from side-chain protected X-VEPNCDIHVMWEWECFERL-Tz4-lfrew,where X is a pegylated reporter tag (e.g., biotin-PEG, DOTA-PEG, etc.)or an N-terminal capping group (e.g., acetyl). The syntheses will beginwith a commercially available pegylated linker consisting of multiple(2, 3, or 4) reactive sites and will follow an amide coupling procedure.

Homomultimeric biligand capture agents may also be synthesized using themethod shown in FIG. 31 for Biligand 2. A multimeric variant will besynthesized from side-chain protectedX-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Az4, where X is a pegylated reporter tag(e.g., biotin-PEG, DOTA-PEG, etc.) or an N-terminal capping group (e.g.,acetyl). The syntheses will begin with a commercially availablepegylated linker consisting of multiple reactive sites. Each site isfirst appended with an alkyne moiety, then conjugated to a capture agentthrough a CuAAC.

Homomultimeric triligand capture agents will also be generated. Forexample, multimeric variants of Triligand 2 may be synthesized fromX-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird, where X is a pegylatedreporter tag (e.g., biotin-PEG, DOTA-PEG, etc.) or an N-terminal cappinggroup (e.g., acetyl). The structure of an exemplary Triligand 2homodimer generated by this method is set forth in FIG. 30. Similarly,multimeric variants of Triligand 2 may be synthesized fromX-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird-Az4, where X is a pegylatedreporter tag (i.e., biotin-PEG, DOTA-PEG, etc.) or an N-terminal cappinggroup (i.e., acetyl), will be synthesized and subsequently evaluated asabove. The structure of an exemplary Triligand 2 homodimer generated bythis method is set forth in FIG. 32.

Heteromultimeric variants of the biligand and triligand capture agentsmay also be synthesized by various methods. For example, a heterodimerof Triligands 2 and 3 as set forth in FIG. 33 may be prepared viacovalent conjugation as described above. A synthetically producedheterodimer (where each peptide of the dimer is different in sequenceand each interacts with a discrete, non-overlapping epitope on a singleprotein) may maximize the improvement in binding affinity and/orreceptor blocking with the appropriate length linker joining the twopeptides.

Multimeric biligands and triligands will be evaluated for improvedaffinity and specificity towards VEGF. Multimeric capture agents willalso be evaluated for improvements in biological activity both in vitro(e.g., displacement of VEGF from VEGF receptor and/or antagonismresulting in decreased cell growth) and in vivo (e.g., reduction ofangiogenesis). Multimeric capture agents may be comparatively evaluatedwith various non-covalent mixtures of capture agents and/or otherpeptides.

Example 14 Synthesis of PEGylated Triligand 2

PEGylated variants of X-Triligand 2 (FIG. 34), where X is a biotin-PEG3linker or N-terminal capping group (e.g., acetyl) were prepared. Usingan amide coupling procedure, Triligand 2 was covalently conjugated to acommercially available PEGylation module that is linear or branched.

Preparation of side-chain protected N-acetyl triligand on CTC resin.X-Triligand 2 was prepared using microwave-assisted Fmoc-based solidphase peptide synthesis (SPPS) on 2-chlorotrityl chloride (CTC) resin.The first amino acid was attached to the resin following the vendor'sprotocol. The resin was transferred to a CEM Liberty 1 microwave peptidesynthesizer for the preparation of the remaining triligand. Each aminoacid coupling reaction incorporated 4 equiv of Fmoc-amino acid, 4 equivof HBTU(O-Benzotriazole-N,N,N′,N′-tetramethyl-uronium-hexafluoro-phosphate),and 10 equiv of N,N-Diisopropylethylamine (DIEA). Deprotection of theFmoc group required 20% piperidine/NMP, followed by wash with NMP.Coupling conditions of the two Tz4 linkers were modified to include 4equiv of Fmoc-amino acid, 4 equiv of HATU(O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluroniumhexafluorophosphate) and 10 equiv of DIEA. Deprotection of the Fmocgroup required 20% piperidine/NMP, followed by wash with NMP.

Option (A): For final N-terminal capping (0.125 mmol scale), the resinwas subjected to a solution of DIEA (1.1 mL), NMP (1.0 mL), and aceticanhydride (0.6 mL). After shaking at room temperature for 30 minutes,the resin was filtered and washed with NMP (3×), DCM (3×) and MeOH (3×).The resin was dried under vacuum for ˜10 min.

Option (B): For the preparation of N-terminal biotinylated triligand,the PEG3 linker and biotin group were coupled to the resin containingtriligand using a CEM Liberty 1 microwave peptide synthesizer. Couplingconditions were 4 equiv of Fmoc containing PEG3 linker, 4 equiv of HBTUand 10 equiv of DIEA. Deprotection of the Fmoc group required 20%piperidine/NMP, followed by wash with NMP. Coupling conditions forbiotin were 4 equiv of biotin dissolved in DMSO/NMP (1:1), 4 equiv ofHBTU and 10 equiv of DIEA. The resin was filtered and washed with NMP(3×), DCM (3×) and MeOH (3×), dried under vacuum for ˜10 minutes.

Cleavage of Side-Chain Protected Triligand from CTC resin (0.25 mmolscale). To the dried side-chain protected triligand resin was added 3-4mL of DCM/TFE (8:2) solution. After stirring at room temperature for 1hour, the resin was filtered through cotton or glass wool into acentrifuge tube containing ˜30 mL cold ether. A white precipitateformed. The resin was washed with 8:2 DCM/TFE until no more precipitateformed (˜3-4 mL). Additional ether was added to a total volume of 50 mL,then the crude product was centrifuged (4500 rpm, 5 min, 4° C.).Following centrifugation, the supernatant was removed and the crudesolid was dried by lyophilization.

Preparation of Ac-Triligand with C-terminal Linear PEG40 PEGylation.Side-chain protected Ac-triligand (125 mg, 17.2 μmol) was added to avial, purged with Ar, and dissolved in anhydrous DMF (0.5 mL). Asolution of 0.5 M HATU/HOAt (34 μL, 17 μmol) and DIEA (2.9 μL, 16.6μmol) were then added and stirred for 15 min at room temperature. Duringthis time, PEG40 amine (100 mg, 2.5 μmol; Jenkem #M-NH2-40K) wasseparately dissolved in anhydrous DCM (0.5 mL). The reaction mixturecontaining Ac-triligand was added to PEG40 amine solution at roomtemperature and then stirred overnight (12-16 hours). This reactionmixture was added dropwise to a centrifuge tube with 30 mL cold ether,resulting in the formation of a white precipitate. After filling thetube to ˜45 mL with cold ether, the sample was centrifuged 3× (4500 rpm,5 min, 4° C.). Following centrifugation, the supernatant was removed andthe crude solid was dried by lyophilization.

Preparation of Ac-Triligand with C-terminal Branched PEG40 PEGylation.Side-chain protected Ac-triligand (125 mg, 17.2 μmol) was added to avial, purged with Ar, and dissolved in anhydrous DMF (0.5 mL). Asolution of 0.5 M HATU/HOAt (34 μL, 17 μmol) and DIEA (2.9 μL, 16.6μmol) were then added and stirred for 15 min at rt. During this time,Y-shape PEG40 amine (100 mg, 2.5 μmol; Jenkem #Y—NH2-40K) was separatelydissolved in anhydrous DCM (0.5 mL). The reaction mixture containingAc-triligand was added to Y-shape PEG40 amine solution at roomtemperature and then stirred overnight (12-16 h). This reaction mixturewas added dropwise to a centrifuge tube with 30 mL cold ether, resultingin the formation of a white precipitate. After filling the tube to −45mL with cold ether, the sample was centrifuged 3× (4500 rpm, 5 min, 4°C.). Following centrifugation, the supernatant was removed and the crudesolid was dried by lyophilization.

Biotinylated PEGylated triligands were prepared by similar methods, butwith a starting material of side-chain protected triligand presenting anN-terminal biotin linker.

Deprotection and Disulfide Cyclization. Each of the crude PEGylatedtriligands (from above) was dissolved in 2.5-3.5 mL ofTFA/H₂O/triisopropylsilane[TIS]/2,2′-(ethylenedioxy)-diethanediol[DODT](92.5/2.5/2.5/2.5) and then stirred at room temperature for 4 hours.Cold ether (˜45 mL) was then added to each tube. Tubes were shakenvigorously and then centrifuged (4500 rpm, 5 minutes, 4° C.). Afterremoving the supernatant, the crude solid was resuspended in another 45mL of cold ether and centrifuged twice more. The final supernatant wasremoved and the crude solid was dried by lyophilization.

For disulfide cyclization, the crude solid was dissolved in 250 μL ofDMSO. After the solid was mostly dissolved, H₂O (2.5 mL) was added andthe pH was adjusted dropwise with ammonium carbonate (5%) solution untilpH 6-7 was reached. This mixture was stirred at room temperature for ≧4hours. This solution was further diluted with methanol and then purifieddirectly by HPLC.

The PEGylation synthesis reactions are summarized in FIGS. 35 and 36.PEGylated triligands will be evaluated for affinity and specificity forVEGF, as well as for biological activity in vitro and in vivo.

Example 15 Triligand Multimerization on Multi-Arm PEGylation Scaffolds

Dimeric and tetrameric variants of X-Triligand 2 (FIG. 34), where X is abiotin-PEG3 linker or N-terminal capping group (e.g., acetyl) wereprepared. Using an amide coupling procedure, Triligand 2 was covalentlyconjugated to a commercially available multi-arm PEGylation linkerconsisting of multiple (two or four) reactive sites.

Preparation of Side-Chain Protected Triligand on CTC Resin.

X-Triligand 2 was prepared using microwave-assisted Fmoc-based solidphase peptide synthesis (SPPS) on 2-chlorotrityl chloride (CTC) resin.The first amino acid was attached to the resin following the vendor'sprotocol. The resin was transferred to a CEM Liberty 1 microwave peptidesynthesizer for the preparation of the remaining triligand. Each aminoacid coupling reaction incorporated 4 equiv of Fmoc-amino acid, 4 equivof HBTU(O-Benzotriazole-N,N,N′,N′-tetramethyl-uronium-hexafluoro-phosphate),and 10 equiv of N,N-Diisopropylethylamine (DIEA). Deprotection of theFmoc group required 20% piperidine/NMP, followed by wash with NMP.Coupling conditions of the two Tz4 linkers were modified to include 4equiv of Fmoc-amino acid, 4 equiv of HATU(O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluroniumhexafluorophosphate) and 10 equiv of DIEA. Deprotection of the Fmocgroup required 20% piperidine/NMP, followed by wash with NMP.

Option (A): For final N-terminal capping (0.125 mmol scale), the resinwas subjected to a solution of DIEA (1.1 mL), NMP (1.0 mL), and aceticanhydride (0.6 mL). After shaking at room temperature for 30 minutes,the resin was filtered and washed with NMP (3×), DCM (3×) and MeOH (3×).The resin was dried under vacuum for ˜10 minutes.

Option (B): For the preparation of N-terminal biotinylated triligand,the PEG3 linker and biotin group were coupled to the resin containingtriligand using a CEM Liberty 1 microwave peptide synthesizer. Couplingconditions were 4 equiv of Fmoc containing PEG3 linker, 4 equiv of HBTUand 10 equiv of DIEA. Deprotection of the Fmoc group required 20%piperidine/NMP, followed by wash with NMP. Coupling conditions forbiotin were 4 equiv of biotin dissolved in DMSO/NMP (1:1), 4 equiv ofHBTU and 10 equiv of DIEA. The resin was filtered and washed with NMP(3×), DCM (3×) and MeOH (3×), dried under vacuum for ˜10 minutes.

Cleavage of Side-Chain Protected Triligand from CTC Resin (0.25 MmolScale).

To the dried side-chain protected triligand resin was added 3-4 mL ofDCM/TFE (8:2) solution. After stirring at room temperature for 1 hour,the resin was filtered through cotton or glass wool into a centrifugetube containing ˜30 mL cold ether. A white precipitate formed. The resinwas washed with 8:2 DCM/TFE until no more precipitate formed (˜3-4 mL).Additional ether was added to a total volume of 50 mL, then the crudeproduct was centrifuged (4500 rpm, 5 minutes, 4° C.). Followingcentrifugation, the supernatant was removed and the crude solid wasdried by lyophilization.

Preparation of Ac-Tetramer.

Side-chain protected Ac-triligand (760 mg, 0.105 mmol) was added to avial, purged with Ar, and dissolved in anhydrous DMF (2.0 mL). HATU (38mg, 0.100 mmol), HOAt (13.6 mg, 0.100 μmol), and DIEA (17 μL, 97.6 μmol)were then added and stirred for 15 min at rt. During this time, 4ARMPEG40 amine (200 mg, 5.0 μmol; Jenkem #4ARM-NH2-40K) was separatelydissolved in anhydrous DCM (1.5 mL). The reaction mixture containingAc-triligand was added to 4ARM PEG40 amine solution at rt, and thenstirred overnight (12-16 hours). This reaction mixture was addeddropwise to two centrifuge tubes with 30 mL cold ether, resulting in theformation of a white precipitate. After filling each tube to −45 mL withcold ether, samples were centrifuged 3× (4500 rpm, 5 min, 4° C.).Following centrifugation, the supernatant was removed and the crudesolid was dried by lyophilization.

Preparation of Ac-Dimer.

Side-chain protected Ac-triligand (208 mg, 28.7 μmol) was added to avial, purged with Ar, and dissolved in anhydrous DMF (2.0 mL). HATU(18.7 mg, 49.2 μmol), HOAt (7.15 mg, 52.5 μmol), and DIEA (8.5 μL, 48.8μmol) were then added and stirred for 15 min at rt. During this time,2ARM PEG7.5 amine (37.5 mg, 5.0 μmol; Jenkem #NH2-PEG7500-NH2) wasseparately dissolved in anhydrous DCM (1.5 mL). The reaction mixturecontaining Ac-triligand was added to 2ARM PEG7.5 amine solution at rt,and then stirred overnight (12-16 hours). This reaction mixture wasadded dropwise to two centrifuge tubes with 30 mL cold ether, resultingin the formation of a white precipitate. After filling each tube to ˜45mL with cold ether, samples were centrifuged 3× (4500 rpm, 5 minutes, 4°C.). Following centrifugation, the supernatant was removed and the crudesolid was dried by lyophilization.

Biotinylated triligand dimers and tetramers were prepared by similarmethods, but with a starting material of side-chain protected triligandpresenting an N-terminal biotin linker.

Deprotection and Disulfide Cyclization.

The crude PEGylated PCC dimer or tetramer (from above) was dissolved in2.5-3.5 mL ofTFA/H₂O/triisopropylsilane[TIS]/2,2′-(ethylenedioxy)-diethanediol[DODT](92.5/2.5/2.5/2.5) and then stirred at room temperature for 4 hours.Cold ether (˜45 mL) was then added to each tube. Tubes were shakenvigorously and then centrifuged (4500 rpm, 5 minutes, 4° C.). Afterremoving the supernatant, the crude solid was resuspended in another 45mL of cold ether and centrifuged twice more. The final supernatant wasremoved and the crude solid was dried by lyophilization.

For disulfide cyclization, the crude solid was dissolved in 250 μL ofDMSO. After the solid was mostly dissolved, H₂O (2.5 mL) was added andthe pH was adjusted dropwise with ammonium carbonate (5%) solution untilpH 6-7 was reached. This mixture was stirred at room temperature for ≧4hours. This solution was further diluted with methanol (2.5 mL or moreif needed) and then purified directly by HPLC.

The multimerization synthesis reactions are summarized in FIGS. 37 and38. PEGylated triligands will be evaluated for affinity and specificityfor VEGF, as well as for biological activity in vitro and in vivo.

Example 16 Evaluation of Triligand Multimerization and Modifications

The C-terminus of a VEGF capture agent provides a potential site formedicinal chemistry optimization. A carboxylic acid terminus (—COOH)would be negatively charged at physiological pH, while a carboxamideterminus (—CONH₂) would be charge-neutral. Depending on the nature ofthe protein epitope targeted by the capture agent, one C-terminus mayhave improved properties over the other.

An in vitro competitive binding assay was performed as set forth inExample 8 using immobilized rhVEGFR2. Triligand 2-COOH displayed ˜4×improvement in blocking over the original Triligand 2 with a carboxamideterminus, with blocking approaching that of multimericstreptavidin-conjugated Triligand 2 (FIG. 39). Multimeric streptavidinconjugates of Triligand 2-COOH and Triligand 2-CONH₂ were found to blocksimilarly (FIG. 39). These results suggest that transforming theC-terminal carboxamide to a C-terminal carboxylic acid in the anti-VEGFtriligand is important for in vitro blocking, but that optimization isimportant for the monomer only. In another competitive bindingexperiment, PEG2arm-Triligand 2 (dimer) displayed enhanced bindingversus monomeric Triligand 2, while blocking by PEG4arm-Triligand 2(tetramer) suggested an additional improvement and approaches theblocking of multimeric streptavidin-conjugated Triligand 2 (FIG. 40).Overall, these results suggest that multimerization may be a dominatinginfluence on blocking, and may arise from both affinity and sizecontributions.

A binding affinity ELISA assay was performed as set forth in Example 3.Multimeric streptavidin-conjugated Triligand 2 and PEG4arm-Triligand 2(tetramer) were found to share similar binding affinity for rhVEGF165(FIG. 41). Further, the affinity of PEG2arm-Triligand 2 (dimer) (KD=˜7.5nM) was lower than that of the tetramer (KD=˜1 nM) but higher than thatof the monomer (KD=˜15 nM) (FIG. 41). These results suggest thatmultimerization and size appear to be critical factors for bindingaffinity.

Pull-down assays and Western blots were performed as described inExample 4 to evaluate binding specificity. VEGF was immunoprecipitatedfrom VEGF-spiked buffer (B) or 25% v/v human serum (S) usingfunctionalized magnetic beads. C-terminal PEGylation was found to have apositive impact on specificity (i.e., less capture of serum proteins),but a negative impact on affinity (i.e., less capture of VEGF) (FIG.42). No difference was observed for the C-terminal amide versus acid.The specificity of PEG2arm-Triligand 2 (dimer) was found to beapproximately the same as the monomer (FIG. 43).

Example 17 Triligand Biodistribution

VEGF triligand was prepared as an N-terminal DOTA conjugate bysolid-phase reaction with DOTA-tris (t-Bu ester) (B-260; Macrocyclics,Dallas, Tex.) prior to release of the peptide from resin andpurification by HPLC. DOTA conjugated Avastin® was generated by reactingAvastin® with DOTA-NHS-ester (Macrocyclics, Dallas, Tex.) in 0.1 MNa₂HPO₄ buffer. After conjugation of Avastin®, reaction mixtures werecentrifuged repeatedly through a YM-30 Centricon® centrifugal filters(Millipore, Billerica, Mass.) with 0.1 M pH 6.5 ammonium citrate bufferto remove unconjugated small molecules. The concentrations of purifiedDOTA conjugates were determined by measuring the absorbance at 280 nm ofa UV spectrophotometer (Eppendorf, Westbury, N.Y.). For radiolabeling,DOTA-conjugated triligand and Avastin® were incubated with ⁶⁴Cu in 0.1 Mammonium citrate, pH 6.5, at 43° C. for one hour. Labeled ⁶⁴Cu-DOTA-testagent was purified by size-exclusion column (Bio-Spin6, BIO-RADLaboratories). Radiochemical purity was determined by integrating areason HPLC. This analysis was conducted on a size-exclusion column andcharacterized by the percentage of radioactivity associated with the 150kDa protein peak.

30 female immunocompromised NU/J mice were obtained from JacksonLaboratories (25 tumor bearing, five non-tumor bearing). All mice wereweighed and subjected to general clinical observations. For tumorbearing mice, subcutaneous human HT29 colon adenocarcinoma tumor cells(VEGF-positive) were implanted on the left rear flank and human MSTO-211H mesothelioma tumor cells (VEGF-negative) were implanted on the rightrear flank. HT29 cells were implanted two weeks after implantation ofMSTO-211 H cells. Co-implantation of VEGF-positive and VEGF− negativetumor cells resulted in asymmetric tumors with localized VEGFexpression.

Fourteen of the mice were selected for the study. These fourteen micewere divided into Groups 1-6. Groups 1 and 2 were non-tumor bearing(three mice in total), while Groups 3-6 were tumor bearing (11 mice intotal). Groups 1-4 and 6 were administered ⁶⁴Cu-DOTA radiolabeled VEGFtriligand either intraperitoneally (IP) (Groups 1, 3, 4, and 6) orintravenously (IV) (Group 2). Positive control mice (Group 5) received⁶⁴Cu-DOTA radiolabeled Avastin® as test agent. Group 6 mice wereadministered IV Avastin® or vehicle control as a blocker 24 hours priorto ⁶⁴Cu-DOTA radiolabeled VEGF triligand, administration. Test agent wasadministered to Group 3 at 1 week, Groups 4 and 5 at 2 weeks, and Group6 at 3 weeks after implantation of HT29 cells. The study protocol issummarized in Table 8.

TABLE 8 Biodistribution study protocol MSTO HT29 tumor tumor Dose masssize mass size Dose ⁶⁴Cu level Mouse at selection at selection volume(μCl/ (μg/ Group Route Test agent ID # (mm³) (mm³)2 (μL) animal) animal)1 IP ⁶⁴Cu-DOTA- 1001 NA NA 240 202.6 64.8 (Pretest) Triligand 1102R NANA 270 193.02 72.9 2 IV ⁶⁴Cu-DOTA- 1003 NA NA 250 167.9 67.5 (Pretest)Triligand 3 IP ⁶⁴Cu-DOTA- 1004 267.696 283.9655 150 193.69 52.5Triligand 1105R 435.896 299.568 170 210.41 66.3 1106R 621.075 340.805230 211.81 89.7 4 IP ⁶⁴Cu-DOTA- 1005 465.7465 539.055 110 208.22 52.8Triligand 1007 744.185 463.736 130 208.12 62.4 1008 793.5 499.023 160203.13 76.8 5 IV ⁶⁴Cu-Avastin 1005 441.8 499.234 250 204.82 52.5(Positive control) 6 IP ⁶⁴Cu-DOTA- 1009 953.344 775.284 100 210.8 47.8(Blocker- Triligand 1011 1230.08 714.07 100 203.47 46.1 vehicle) 6 10101131.588 707.868 110 215.06 52.1 (Blocker- 1012 1139.9085 697.632 110208.91 50.6 Avastin)

After dosing, mice were individually housed in suspended stainless steelwire mesh cages. Mice were fed irradiated block PicoLab Diet Rodent Diet20 #5K75 (PMI Nutrition International, Inc.) ad libitum. Body weight wasmeasured prior to biligand/triligand administration and weeklythereafter. Tumor size (length and width) was measured by caliper priorto administration and three times per week thereafter. Tumor volumeswere calculated by the formula: Tumor volume=Length×Width²/2, wherelength was always the longer dimension. Where there was more than onetumor per mouse, the location and dimensions of all tumors was recordedon a mass map.

Biodistribution was evaluated by MicroPET/CT imaging using dynamicand/or static scans. A CT scan preceded the first PET scan in eachanimal. Groups 1-4 and 6 were subjected to a dynamic PET scan at 0 to 2hours after administration, and static scans at 4 and 20 hours afteradministration. Group 5 was subjected to a single static scan at 20hours after administration. Static scans at 4 hours were performed for15 minutes, while static scans at 20 hours were performed for 30minutes. At the completion of scanning (approximately 21 hours aftertest agent administration), mice from Groups 1-4 and 6 were sacrificedfor tissue biodistribution analysis. The following tissues werecollected: tumors (groups 3, 4, and 6 only), liver, spleen, kidney,blood, muscle, heart, bladder, gall bladder, brain, femur, and lung.Tissues were weighed and counted for radioactivity concentration using agamma counter or dose calibrator. Two samples of the remaining testarticle formulation equivalent to one thousandth of the injectedradioactivity dose was also counted using the gamma counter and used areference standard. Radioactivity was normalized by organ/tissue weight.

Biodistribution results for animal 1102R (Group 1) and 1004 (Group 3)are set forth in FIGS. 48 and 49, respectively.

Tissue distribution data at 4 and 20 h post injection suggest that⁶⁴Cu-DOTA-triligand accumulates in the tumor as a function of time (FIG.74).

Biodistribution results for animals 1009-1012 (Group 6) are set forth inFIGS. 44-47, respectively. A side-by-side comparison of the non-blockademice (1009 and 1011) and the Avastin® blockade mice (1010 and 1012) isset forth in FIG. 57. These results show that pre-treatment withAvastin® decreases the intensity of VEGF triligand signal in HT29tumors, which further supports the results from Example 9 suggestingthat Avastin® and the VEGF triligand bind a shared epitope.

Example 18 Triligand Biodistribution

The in vitro binding affinity and blockade of VEGF receptor:ligandinteractions by peptides synthesized using PCC technology suggested thatsimilar molecular interactions may be modulated in vivo by the VEGFbiligands and triligands disclosed herein. As shown in Example 17,pre-treatment with Avastin® decreased VEGF triligand signal in vivo inan HT29 mouse model. To further evaluate this effect, a follow-upbiodistribution experiment was performed to phenotype VEGF expressed byHT29 xenografts in a murine model.

Radiolabeled VEGF triligand and HT-29 mice were prepared as describedabove in Example 17. After tumors had achieved sufficient volume, fourcontrol mice (mice 1013, 1015, 1016, and 1114R) were IV administeredvehicle control, while test mice were IV administered Avastin® in molarexcess. After 24 hours (test mice 1014, 1017, and 1018) or 48 hours(test mice 1021, 1022, 1023, and 1024), mice were IP administeredradiolabeled VEGF triligand (˜65 μg, 3.4 μCi/μg). Biodistribution wasevaluated by MicroPET/CT imaging using a static scan at 0, 4, and 20hours after triligand administration.

Biodistribution results for animals 1013 (control), 1014 (24 hourblockade), 1017 (24 hour blockade), 1018 (24 hour blockade), 1021 (48hour blockade), and 1022 (48 hour blockade) are set forth in FIGS.58-63, respectively. Additional biodistribution results for animals1114R (control), 1017, and 1022 are set forth in FIGS. 51-53,respectively. A side-by-side comparison of the control mice and the 48hour blockade mice at 20 hours is set forth in FIG. 54. These resultsshow that Avastin® blockade attenuates tumor binding by the VEGFtriligand, suggesting that Avastin® and the VEGF triligand bind a sharedepitope.

At the completion of scanning, mice were sacrificed for tissuebiodistribution analysis as described above in Example 17. FIG. 55summarizes the results for tumor versus heart tissue samples. Thereduction in VEGF triligand uptake in tumor tissue was 29% with 24 hourAvastin® blockade and 27% with 48 hour Avastin® blockade, with aMann-Whitney non-parametric p-value of 0.004. The reduction in hearttissue, on the other hand, was only 11% with 24 hour Avastin® blockadeand 0% with 48 hour Avastin® blockade, with a p-value of 0.933. Resultsacross all tissue types are set forth in FIG. 56. These results showthat although ⁶⁴Cu was detectable in the bladder, blood, brain, femur,gallbladder, heart, kidney, liver, lung, muscle, and spleen,pre-administration of Avastin® only resulted in ⁶⁴Cu signal attenuationin tumor tissue.

HT29 tumors suggest that VEGF triligand binds specifically to hVEGFexpressed in vivo. Detection of the ⁶⁴Cu signal in the other 11 tissueswithout Avastin® attenuation suggests non-specific localization of theVEGF triligand. However, these data are similar to those reported formetal-chelated Avastin® in similar studies of VEGF-overexpressing humantumors in murine xenograft models (Nagengast 2011; Paudyal 2011). Thedata suggest the potential for either non-specific binding ofVEGF-epitope targeting proteins, binding to other VEGF isoforms, ororgan-specific clearance, as demonstrated by the kidney signals. Theseresults suggest that the VEGF triligands disclosed herein may be used inclinical applications such as in vivo molecular tumor epitopephenotyping, e.g. “molecular imaging,” which may be beneficial inpatient and tumor stratification for therapeutic decision-making.

Example 19 Plasma Concentrations and Pharmacokinetics of VEGF-PCCFollowing a Single Intravenous (IV) or Intraperitoneal (IP) Dose in MiceMaterials and Methods Test Article

Test article: VEGF-PCC (IN-VT-1001 Triligand) (PCC monomer)Ac-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird. The underlined regioninclusive of the Cys residues is cyclized by a disulfide bond,Ac=N-terminal acetylation, and Tz4=1,4-disubstituted 1,2,3-triazole.

Storage condition: Approximately −20° C.

Samples and Storage

Samples were received from the sponsor on 20 March and 10 Apr. 2012 andstored at approximately −70° C. before and after analysis.

LC-MS/MS Analysis Sample Analysis

The LC-MS/MS system for analysis was comprised of an Agilent 1200 highperformance liquid chromatography (HPLC) and a 5500 Qtrap massspectrometer (Applied Biosystems by Life Technologies, Carlsbad,Calif.).

Concentrations of VEGF-PCC in mouse plasma were determined using anon-validated LC MS/MS assay with Angiotensin I as the internal standardfollowing a solid phase extraction method. Individual VEGF-PCCcalibration and QC standards were prepared from the respectiveintermediate stock solutions by addition to naïve mouse plasma. Thetarget working range of the calibration curve was 50 to 5,000 ng/mL inplasma and the target concentrations of the QC standards were 150 to3,750 ng/mL in plasma for VEGF-PCC.

Batch 1

Calibration curves for VEGF-PCC in mouse plasma ranged from 50 to 5,000ng/mL, with a correlation coefficient value of 0.9936.

Duplicate QC samples at concentrations ranging from 150 to 3,750 ng/mLin mouse plasma were included in the analysis group. In addition,duplicate dilution (10-fold) QC samples at a concentration of 20,000ng/mL in mouse plasma were also included in the analysis group.

The assay lower limit of quantitation (LLOQ) for VEGF-PCC in mouseplasma was 50 ng/mL for Batch 1.

Batch 2

Calibration curves for VEGF-PCC in mouse plasma ranged from 100 to 5,000ng/mL, with a correlation coefficient value of 0.9915.

Duplicate QC samples at concentrations ranging from 150 to 3,750 ng/mLin mouse plasma were included in the analysis group. In addition,duplicate dilution (10-fold) QC samples at a concentration of 20,000ng/mL in mouse plasma were also included in the analysis group.

The assay lower limit of quantitation (LLOQ) for VEGF-PCC in mouseplasma was 100 ng/mL for Batch 2.

The calibration and QC results were evaluated and, based on review bythe study director, it was concluded that the method performance wasacceptable. Data for calibration standards and QC samples are presentedin Appendix 1.

Concentrations of Test Article

Concentrations of VEGF-PCC in mouse plasma are presented in Tables A andB and are presented graphically in FIG. 64. A representativechromatogram is presented in FIG. 75.

TABLE A Plasma concentrations of IN-VT-1001 (ng/mL) in mouse plasmafollowing a single intravenous dose Animal Collection Time Point(Minutes Postdose) Number 3 10 30 60 120 240 360 1440 46 14200 47 1620048 12000 40 7220 41 7550 42 6110 34 2170 35 2210 36 3420 28 1840 29 238030 1870 22 551 23 400 24 514 16 BLQ 17 BLQ 18 BLQ 10 BLQ 11 BLQ 12 BLQ 4BLQ 5 BLQ 6 BLQ Mean 14100 6960 2600 2030 488 0.00 0.00 0.00 SD 2100 754710 303 78.7 0.00 0.00 0.00

TABLE B Plasma concentrations of IN-VT-1001 (ng/mL) in mouse plasmafollowing a single intraperitoneal dose Animal Collection Time Point(Minutes Postdose) Number 10 30 60 120 240 360 480 1440 43 17500 4417000 45 13400 37 19400 38 20200 39 BLQ 31 10800 32 23900 33 11500 25BLQ 26 4730 27 3640 19 259 20 807 21 BLQ 13 390 14 BLQ 15 BLQ 7 BLQ 8BLQ 9 BLQ 1 BLQ 2 BLQ 3 BLQ Mean 16000 13200 15400 2790 355 130 0.000.00 SD 2240 11400 7370 2480 412 225 0.00 0.00

Batch 1

Intravenous samples at 3, 10, and 30 minutes and intraperitoneal samplesat 10, 30, and 60 minutes were diluted 10-fold with naïve mouse plasmaprior to extraction and analysis. All other samples were extracted andanalyzed undiluted.

One intraperitoneal sample at 120 minutes was above the upper limit ofquantitation (ULOQ) for VEGF-PCC (5,000 ng/mL).

Batch 2

The one sample that was above the ULOQ from Batch 1 was diluted 10-foldand re analyzed in Batch 2 where it was now within the calibration curverange.

Pharmacokinetics Intravenous

Mice received a single IV dose of VEGF-PCC at 1 mg/kg. A summary of theplasma concentrations for individual animals is shown in Table A. Plasmapharmacokinetic parameters are listed in Table 9.

TABLE 9 Mean pharmacokinetic parameters for VEGF-PCC in mouse plasmafollowing a single intravenous or intraperitoneal dose Dose DoseAUC_(0-t) AUC_(inf) AUC % CL F T_(1/2) C₀ C_(max) T_(max) V_(SS) Route(mg/kg) (hr*ng/mL) (hr*ng/mL) Ext (%) (mL/min/kg) (%) (hr) (ng/mL)(ng/mL) (hr) (L/kg) IV 1 6070 6490 6.49 2.57 NA 0.598 19100 NA NA 0.0967IP 5 31500 32200 2.04 NA 99 NA NA 19800 0.50 NA NA Not applicable

The mean plasma concentration vs. time curve is shown in FIG. 64.

The mean systemic plasma clearance (CL) and steady state volume ofdistribution (Vss) values for VEGF-PCC following single IV doseadministration at 1 mg/kg were 2.57 mL/min/kg and 0.0967 L/kg,respectively. The mean half-life (t1/2) was 0.598 hours.

The mean back-calculated C0 for VEGF-PCC was 19,100 ng/mL. Thetheoretical C0 for VEGF-PCC [assuming a mean IV dose of 1 mg/kg and anaverage body weight of 33 g and assuming a mean blood volume ofapproximately 1.7 mL (Davies and Morris, 1993)] was approximately 19,400ng/mL.

Intraperitoneal

Mice received a single IP dose of VEGF-PCC at 5 mg/kg. A summary of theplasma concentrations for individual animals is shown in Table B. Plasmapharmacokinetic parameters are listed in Table 9. The mean plasmaconcentration vs. time curve is shown in FIG. 64.

The mean plasma exposure (AUCinf) of VEGF-PCC at 5 mg/kg was 32,200ng*hr/mL. The mean Cmax and corresponding Tmax values were 19,800 ng/mLand 0.50 hours, respectively. The relative bioavailability of VEGF-PCCat 5 mg/kg IP in mice was approximately 99%.

CONCLUSIONS

The purpose of this study was to determine plasma concentrations andpharmacokinetics of VEGF-PCC in mice following a single IV or IP dose ofVEGF-PCC at 1 or 5 mg/kg, respectively, using a liquid chromatographywith tandem mass spectrometric (LC MS/MS) method.

Samples were analyzed using a non-validated LC-MS/MS method. Plasmaconcentrations of VEGF-PCC were determined using a non-validated LCMS/MS assay following a solid phase extraction method. The working rangeof the calibration curve was 50 to 5,000 ng/mL in plasma for VEGF-PCC.

Mice received a single IV dose of VEGF-PCC at 1 mg/kg. The mean systemicplasma clearance (CL) and steady state volume of distribution (Vss)values for were 2.57 mL/min/kg and 0.0967 L/kg, respectively. The meanhalf-life (t1/2) was 0.598 hours. The mean back-calculated CO forVEGF-PCC was 19,100 ng/mL. The theoretical CO for VEGF-PCC [assuming amean intravenous dose of 1 mg/kg and an average body weight of 33 g andassuming a mean blood volume of approximately 1.7 mL (Davies and Morris,1993)] was approximately 19,400 ng/mL.

Mice received a single IP dose of VEGF-PCC at 5 mg/kg. The mean plasmaexposure (AUCinf) of VEGF-PCC at 5 mg/kg was 32,200 ng*hr/mL. The meanCmax and corresponding Tmax values were 19,800 ng/mL and 0.50 hours,respectively. The relative bioavailability of VEGF-PCC at 5 mg/kg IP inmice was approximately 99%.

Example 20 Iterative In Situ Click Chemistry Produces a VEGF-TargetedCapture Agent for in Vivo Molecular Imaging

The development of Protein-Catalyzed Capture agents (PCCs) against VEGFbegan with a phage display-derived peptide that was previouslydemonstrated to interact at the receptor-binding domain.1 The peptidewas modified with a pendant azide at the C-terminus to provide theanchor ligand X-VEPNCDIHVMWEWECFERL-Az4 [where Az4=L-azidolysine,X=biotin-PEGS linker or N-terminal capping group (i.e., acetyl), andunderlined=cyclized]. PEGS was attached asN-Fmoc-N″-succinyl-4,7,10-trioxa-1,13-tridecanediamine (Sigma-Aldrich,671517-5G). N-terminal capping was by acetic anhydride. Intramoleculardisulfide cyclization was run over 4-16 h in 0.05 M ammonium acetate+10%(v/v) DMSO at pH 7-8 (adjusted accordingly with 5% (w/v) aq. ammoniumcarbonate).

Biligands and triligands discovered by the target-guided in situ clickchemistry screens were prepared in bulk by solid-phase synthesis [whereTz4=1,4-disubstituted 1,2,3-triazole linker, FIG. 65], purified byRP-HPLC, and analyzed by mass spectrometry prior to assaying for invitro or in vivo binding to VEGF.

X-VEPNCDIHVMWEWECFERL-Az4. For X=acetyl, MALDI-MS (m/z): calcd. forC117H165N31O33S3 (M+) 2628.1. found 2628.7. For X=biotin-PEGS, MALDI-MS(m/z): calcd. for C139H203N35O39S4 (M+) 3114.4. found 3114.5.

X-VEPNCDIHVMWEWECFERL-Tz4-rplir. For X=acetyl, MALDI-MS (m/z): calcd.for C151H226N44O39S3 (M+) 3375.6. found 3375.8. For X=biotin-PEGS,MALDI-MS (m/z): calcd. for C173H264N48O45S4 (M+) 3861.9. found 3861.4.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew. For X=acetyl, MALDI-MS (m/z): calcd.for C159H222N42O41S3 (M+) 3471.6. found (M+H) 3473.3. For X=biotin-PEGS,MALDI-MS (m/z): calcd. for C181 H260N46O47S4 (M+) 3957.8. found 3957.1.

Biotin-PEGS-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Az4. MALDI-MS (m/z): calcd.for C187H270N50O48S4 (M+) 4112.9. found (M+H) 4115.0.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird. For X=acetyl, MALDI-MS (m/z):calcd. for C196H281N55O55S3 (M+) 4382.0. found (M+H) 4383.3. ForX=biotin-PEGS, MALDI-MS (m/z): calcd. for C218H319N59O61S4 (M+) 4867.3.found 4870.6.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-frsvn. For X=acetyl, MALDI-MS (m/z):calcd. for C197H280N56O51S3 (M+) 4343.0. found (M+Na) 4368.0. ForX=biotin-PEG3, MALDI-MS (m/z): calcd. for C219H318N60O57S4 (M+) 4828.3.found 4830.6.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-hthwl. For X=acetyl, MALDI-MS (m/z):calcd. for C203H281N57O50S3 (M+) 4413.0. found (M+H) 4415.2.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-ewsrw. For X=acetyl, MALDI-MS (m/z):calcd. for C206H283N57O52S3 (M+) 4483.0. found (M+H) 4484.6. ForX=biotin-PEG3, MALDI-MS (m/z): calcd. for C228H321N61O58S4 (M+) 4969.3.found (M+K) 5008.0.

DOTA-PEGS-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird. N-terminalconjugation of DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaceticacid) proceeded by solid-phase reaction with DOTA-tris (t-Bu ester)(B-260; Macrocyclics, Dallas, Tex.) followed by release of the peptidefrom resin and purification by RP-HPLC. MALDI-MS (m/z): calcd. forC224H331N61O66S3 (M+) 5027.4. found (M+H) 5030.7.

Multimeric PCC variants were designed and synthesized to explore thepotential added benefit(s) from increased size and/or valency. Reactionof the C-terminus of the triligand with a 4-arm PEG derivative (MW40,000; Jenkem #4ARM-NH2-40K) resulted in the formation of ahomotetramer (FIG. 76). The homotetramer was purified by RP-HPLC andcharacterized by SDS-PAGE prior to assaying for in vitro binding toVEGF.

X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird homotetramer. A molecularweight of 57,500 Da for X=acetyl or 59,500 Da for X=biotin-PEGS wasexpected by 7.5% SDS-PAGE. Samples prepared in reducing Laemmli bufferwere subjected to electrophoretic separation at 200 V for 30 min in1×TGS (25 mM Tris, 192 mM Glycine, 0.1% SDS (w/v), pH 8.3) for duplicategels. One gel was stained with Bio-Safe Coomassie (Bio-Rad, #161-0786)for 1 h to visualize the peptide-containing bands, while the other gelwas stained with 5% (w/v) aq. barium chloride and then 0.05 M aq. iodineto visualize the PEG-containing bands. Homotetramers were detected byboth stains and confirmed at the expected molecular weights.

For the biotinylated homotetramer, a third 7.5% gel was subsequentlyelectrophoretically transferred to a nitrocellulose membrane in 25 mMTris, 192 mM Glycine, pH 8.3, containing 20% (v/v) methanol (Bio-RadLaboratories, Hercules, Calif.) at 100 V for 30 min. Following transfer,the nitrocellulose membrane was blocked at 4° C. for 2 h in 5% non-fatdry milk in TBS and probed with Streptavidin-HRP (Abcam, ab7403) forconfirmation of the biotin label.

As stated above, the foregoing are merely intended to illustrate thevarious embodiments of the present invention. As such, the specificmodifications discussed above are not to be construed as limitations onthe scope of the invention. It will be apparent to one skilled in theart that various equivalents, changes, and modifications may be madewithout departing from the scope of the invention, and it is understoodthat such equivalent embodiments are to be included herein. Allreferences cited herein are incorporated by reference as if fully setforth herein.

REFERENCES

-   1. Agnew Angew Chem Int Ed Engl 48:4944 (2009)-   2. Bell Cancer Lett 289:81 (2010)-   3. Erlanson Proc Natl Acad Sci USA 97:9367 (2000)-   4. Fairbrother Biochem 37:17754 (1998)-   5. Fields Int J Pept Prot Res 35:161 (1990)-   6. Hosten Drug Metab Dispos 36:1729 (2008)-   7. Jencks Proc Natl Acad Sci USA 78:4046 (1981)-   8. Kwong J Am Chem Soc 131:9695 (2009)-   9. Lam Nature 354:82 (1991)-   10. Lee J Comb Chem 10:807 (2008)-   11. Lee Anal Chem 82:672 (2010)-   12. Liang J Biol Chem 281:951 (2006)-   13. Manetsch J Am Chem Soc 126:12809 (2004)-   14. Mocharla Angew Chem Int Ed Engl 44:116 (2004)-   15. Murray J Comput Aided Mol Des 16:741 (2002)-   16. Nagengast Eur J Cancer 47:1595 (2011)-   17. Pakkala J Pept Sci 13:348 (2007)-   18. Paudyal Cancer Sci 102:117 (2011)-   19. Shi Bioconjug Chem 20:750 (2009)-   20. Shuker Science 274:1531 (1996)-   21. Stollman Int J Cancer 122:2310 (2008)-   22. Watt Anal Chem 72:979 (2000)-   23. Whiting Angew Chem Int Ed Engl 45:1435 (2006)-   24. Fairbrother, W. J.; Christinger, H. W.; Cochran, A. G.; Fuh, G.;    Keenan, C. J.; Quan, C.; Shriver, S. K.; Tom, J. Y. K.; Wells, J.    A.; Cunningham, B. C. Biochemistry 1998, 37, 17754-17764.-   25. (a) Zimmerman, S. B.; Murphy, L. D. Anal. Biochem. 1996, 234,    190-193. (b) Kurfürst, M. M. Anal. Biochem. 1992, 200, 244-248.-   26. Dhara, D.; Chatterji, P. R. J. Phys. Chem. B 1999, 103,    8458-8461.

1-28. (canceled)
 29. A stable, synthetic capture agent that specificallybinds VEGF, wherein the capture agent comprises a designed anchorligand, a designed secondary ligand, a designed tertiary ligand, and afourth VEGF-binding moiety; wherein the anchor ligand, secondary ligand,and tertiary ligand selectively bind VEGF; wherein the anchor ligandcomprises an amino acid sequence 95% identical to the amino acidsequence of SEQ ID NO:1; wherein the secondary ligand comprises aformula of X2-X3-X4-X5-X6, wherein X2 is selected from the groupconsisting of D-arginine, D-tryptophan, D-leucine, D-valine, glycine,D-proline, D-isoleucine and D-alanine; wherein X3 is selected from thegroup consisting of D-proline, D-phenylalanine, glycine, D-arginine,D-lysine, D-histidine, D-tryptophan and D-tyrosine; wherein X4 isselected from the group consisting of D-isoleucine, D-leucine,D-proline, D-alanine, D-arginine, D-phenylalanine, D-threonine andD-histidine; wherein X5 is selected from the group consisting ofD-isoleucine, glycine, D-valine, D-leucine, D-alanine, D-proline,D-lysine, D-glutamate, D-histidine and D-arginine; and wherein X6 isselected from the group consisting of D-arginine, D-lysine,D-tryptophan, D-tyrosine, D-proline, D-valine, glycine, D-isoleucine,D-alanine and D-glutamine; and wherein the tertiary ligand comprises aformula of X2-X3-X4-X5-X6, wherein: X2 is selected from the groupconsisting of D-histidine, D-arginine and D-lysine; X3 is selected fromthe group consisting of D-threonine, D-asparagine, D-leucine, D-proline,D-isoleucine, D-alanine, and D-glutamate; X4 is selected from the groupconsisting of D-histidine, D-lysine, D-arginine, D-tryptophan,D-phenylalanine, D-proline, D-leucine and D-tyrosine; X5 is selectedfrom the group consisting of D-valine, D-proline, D-histidine,D-phenylalanine, D-tryptophan, D-asparagine, D-glutamine, D-serine andD-tyrosine; and X6 is selected from the group consisting of D-arginine,D-tyrosine, D-asparagine, D-glutamine, D-leucine, D-proline, D-lysineand D-histidine; X2 is selected from the group consisting of D-tyrosine,D-phenylalanine and D-tryptophan; X3 is selected from the groupconsisting of D-proline, D-alanine, glycine, D-leucine, D-lysine,D-arginine and D-histidine; X4 is selected from the group consisting ofD-arginine, D-histidine, D-tryptophan, D-phenylalanine, D-glutamate,D-proline, D-serine and D-threonine; X5 is selected from the groupconsisting of D-proline, D-aspartate, D-lysine, D-arginine, D-tyrosine,D-histidine, D-alanine, D-valine, D-leucine and D-asparagine; and X6 isselected from the group consisting of D-histidine, D-lysine,D-asparagine, D-threonine, D-glutamine, D-leucine, D-aspartate,D-serine, D-tyrosine, D-arginine, D-tryptophan, D-glutamate andD-valine; or X2 is selected from the group consisting of D-glutamate andD-aspartate; X3 is selected from the group consisting of D-glutamate,D-phenylalanine, D-tryptophan, D-histidine, D-lysine, D-asparagine andD-serine; X4 is selected from the group consisting of D-isoleucine,D-proline, D-alanine, D-arginine, D-serine, D-aspartate, D-asparagine,D-proline, D-phenylalanine, D-tyrosine and D-histidine; X5 is selectedfrom the group consisting of D-arginine, D-tyrosine, glycine,D-tryptophan, D-lysine, D-histidine, D-alanine, D-asparagine andD-leucine; and X6 is selected from the group consisting of D-aspartate,D-proline, D-tryptophan, D-tyrosine, D-leucine, D-asparagine, D-serineand D-threonine.
 30. The capture agent of claim 29, wherein the anchorligand and the secondary ligand are linked together via a1,4-substituted-1,2,3-triazole residue (Tz4).
 31. The capture agent ofclaim 29, wherein the secondary ligand and tertiary ligand are linkedtogether via a 1,4-substituted-1,2,3-triazole residue (Tz4).
 32. Thecapture agent of claim 29, wherein the fourth VEGF-binding moietycomprises a scaffold that is bound to two or more ligands, wherein eachligand binds VEGF.
 33. The capture agent of claim 32, wherein the fourthVEGF-binding moiety comprises a streptavidin scaffold that isnon-covalently bound to four biotinylated capture agents.
 34. Thecapture agent of claim 33, wherein the fourth VEGF-binding moietycomprises a four-arm PEGylation linker that is covalently bound to fourcapture agents.
 35. The capture agent of claim 33 having the structure:

wherein each PCC is:

wherein X is a pegylated reporter tag or an N-terminal capping group.36. The capture agent of claim 33 having the structure:

wherein

is streptavidin, and each

is: X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird, wherein X is biotin PEG.37. A stable, synthetic, multimeric capture agent that specificallybinds VEGF, wherein the capture agent comprises four, six or twelvepeptide ligands including a designed anchor ligand, a designed secondaryligand and, optionally, a designed tertiary ligand; wherein the anchorligand, secondary ligand, and tertiary ligand selectively bind VEGF;wherein the anchor ligand comprises an amino acid sequence 95% identicalto the amino acid sequence of SEQ ID NO:1; wherein the secondary ligandcomprises a formula of X2-X3-X4-X5-X6, wherein X2 is selected from thegroup consisting of D-arginine, D-tryptophan, D-leucine, D-valine,glycine, D-proline, D-isoleucine and D-alanine; wherein X3 is selectedfrom the group consisting of D-proline, D-phenylalanine, glycine,D-arginine, D-lysine, D-histidine, D-tryptophan and D-tyrosine; whereinX4 is selected from the group consisting of D-isoleucine, D-leucine,D-proline, D-alanine, D-arginine, D-phenylalanine, D-threonine andD-histidine; wherein X5 is selected from the group consisting ofD-isoleucine, glycine, D-valine, D-leucine, D-alanine, D-proline,D-lysine, D-glutamate, D-histidine and D-arginine; and wherein X6 isselected from the group consisting of D-arginine, D-lysine,D-tryptophan, D-tyrosine, D-proline, D-valine, glycine, D-isoleucine,D-alanine and D-glutamine; and wherein the tertiary ligand comprises aformula of X2-X3-X4-X5-X6, wherein: X2 is selected from the groupconsisting of D-histidine, D-arginine and D-lysine; X3 is selected fromthe group consisting of D-threonine, D-asparagine, D-leucine, D-proline,D-isoleucine, D-alanine, and D-glutamate; X4 is selected from the groupconsisting of D-histidine, D-lysine, D-arginine, D-tryptophan,D-phenylalanine, D-proline, D-leucine and D-tyrosine; X5 is selectedfrom the group consisting of D-valine, D-proline, D-histidine,D-phenylalanine, D-tryptophan, D-asparagine, D-glutamine, D-serine andD-tyrosine; and X6 is selected from the group consisting of D-arginine,D-tyrosine, D-asparagine, D-glutamine, D-leucine, D-proline, D-lysineand D-histidine; X2 is selected from the group consisting of D-tyrosine,D-phenylalanine and D-tryptophan; X3 is selected from the groupconsisting of D-proline, D-alanine, glycine, D-leucine, D-lysine,D-arginine and D-histidine; X4 is selected from the group consisting ofD-arginine, D-histidine, D-tryptophan, D-phenylalanine, D-glutamate,D-proline, D-serine and D-threonine; X5 is selected from the groupconsisting of D-proline, D-aspartate, D-lysine, D-arginine, D-tyrosine,D-histidine, D-alanine, D-valine, D-leucine and D-asparagine; and X6 isselected from the group consisting of D-histidine, D-lysine,D-asparagine, D-threonine, D-glutamine, D-leucine, D-aspartate,D-serine, D-tyrosine, D-arginine, D-tryptophan, D-glutamate andD-valine; or X2 is selected from the group consisting of D-glutamate andD-aspartate; X3 is selected from the group consisting of D-glutamate,D-phenylalanine, D-tryptophan, D-histidine, D-lysine, D-asparagine andD-serine; X4 is selected from the group consisting of D-isoleucine,D-proline, D-alanine, D-arginine, D-serine, D-aspartate, D-asparagine,D-proline, D-phenylalanine, D-tyrosine and D-histidine; X5 is selectedfrom the group consisting of D-arginine, D-tyrosine, glycine,D-tryptophan, D-lysine, D-histidine, D-alanine, D-asparagine andD-leucine; and X6 is selected from the group consisting of D-aspartate,D-proline, D-tryptophan, D-tyrosine, D-leucine, D-asparagine, D-serineand D-threonine.
 38. The capture agent of claim 37, wherein the anchorligand and the secondary ligand are linked together via a1,4-substituted-1,2,3-triazole residue (Tz4).
 39. The capture agent ofclaim 37, wherein the secondary ligand and tertiary ligand are linkedtogether via a 1,4-substituted-1,2,3-triazole residue (Tz4).
 40. Thecapture agent of claim 37, wherein the capture agent is homomultimeric.41. The capture agent of claim 37, wherein the capture agent isheteromultimeric.
 42. The capture agent of claim 41, wherein eachpeptide is different in sequence and interacts with a discrete,non-overlapping epitope on VEGF.
 43. The capture agent of claim 37,comprising four peptide ligands.
 44. The capture agent of claim 43selected from the group consisting of:

wherein

is a pegylated linker, R is a pegylated reporter tag or an N-terminalcapping group.
 45. The capture agent of claim 37, comprising six peptideligands.
 46. The capture agent of claim 45 having a structure selectedfrom the group consisting of:

and

wherein each PCC is:

and each X is a pegylated reporter tag or an N-terminal capping group.47. The capture agent of claim 37, comprising twelve peptide ligands.48. The capture agent of claim 47 having the structure:

wherein each PCC is:

wherein X is a pegylated reporter tag or an N-terminal capping group.49. The capture agent of claim 47 having the structure:

wherein

is streptavidin, and each

is: X-VEPNCDIHVMWEWECFERL-Tz4-lfrew-Tz4-eeird, wherein X is biotin PEG.50. The capture agent of claim 29 or claim 37, wherein the capture agentis labeled with a detection label.
 51. A method of detecting VEGF in abiological sample using an immunoassay, wherein the immunoassay utilizesa capture agent of claim 29 or claim 37, and wherein said capture agentreplaces an antibody or its equivalent in the immunoassay.
 52. Themethod of claim 51, wherein the immunoassay is selected from the groupof Western blot, pull-down assay, dot blot, and ELISA.
 53. A method oftreating a condition associated with increased VEGF expression and/oractivity in a subject in need thereof, comprising administering atherapeutically effective amount of a capture agent of claim 1 or claim9.
 54. The method of claim 53, wherein said condition is selected fromthe group consisting of cancer, proliferative retinopathy, diseasepathology of wet form age-related macular degeneration (AMD), orrheumatoid arthritis.
 55. A method of inhibiting VEGF activity in asubject comprising administering to the subject a therapeuticallyeffective amount of the capture agent of claim 29 or claim 37.